rs754825722

Variant names:

• chr19-55518206-C-A
• rs754825722
• NM_001144950.2:c.3930C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-55518206-C-A
• chr19-55518206-C-G
• chr19-55518206-C-T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The ENST00000389623.11(SSC5D):​c.3930C>A​(p.Thr1310Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T1310T) has been classified as Benign.

• Frequency:
  • Genomes: 𝑓 0.0000090 (0 hom., cov: 21)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SSC5D ENST00000389623.11 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 0 publications found

Genes affected

SSC5D (HGNC:26641): (scavenger receptor cysteine rich family member with 5 domains) Predicted to enable fibronectin binding activity; laminin binding activity; and scavenger receptor activity. Predicted to be involved in defense response; detection of bacterial lipoprotein; and negative regulation of interleukin-8 production. Predicted to act upstream of or within regulation of interleukin-8 production. Predicted to be located in collagen-containing extracellular matrix. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000300360 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP7: Synonymous conserved (PhyloP=0.014 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000389623.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSC5D	NM_001144950.2	MANE Select	c.3930C>A	p.Thr1310Thr	synonymous	Exon 14 of 14	NP_001138422.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSC5D	ENST00000389623.11	TSL:1 MANE Select	c.3930C>A	p.Thr1310Thr	synonymous	Exon 14 of 14	ENSP00000374274.4
	ENSG00000300360	ENST00000771167.1		n.231+2566G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000904 AC: 1 AN: 110626 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000330

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1314798 Hom.: 0 Cov.: 75 AF XY: 0.00 AC XY: 0 AN XY: 648048

African (AFR) AF: 0.00 AC: 0 AN: 27428

American (AMR) AF: 0.00 AC: 0 AN: 29914

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22586

East Asian (EAS) AF: 0.00 AC: 0 AN: 30030

South Asian (SAS) AF: 0.00 AC: 0 AN: 76030

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44532

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5396

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1025532

Other (OTH) AF: 0.00 AC: 0 AN: 53350

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000904 AC: 1 AN: 110626 Hom.: 0 Cov.: 21 AF XY: 0.0000186 AC XY: 1 AN XY: 53714

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 22050

American (AMR) AF: 0.00 AC: 0 AN: 10136

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2888

East Asian (EAS) AF: 0.000330 AC: 1 AN: 3030

South Asian (SAS) AF: 0.00 AC: 0 AN: 4312

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7844

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 232

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 57770

Other (OTH) AF: 0.00 AC: 0 AN: 1518

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.75
DANN	Benign	0.43
PhyloP100		0.014

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs754825722; hg19: chr19-56029573;