8-27681853-T-C

Position:

• chr8-27681853-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017013536.3(SCARA3):​c.1370-16339T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,122 control chromosomes in the GnomAD database, including 27,948 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (27948 hom., cov: 33)
• Consequence: SCARA3 XM_017013536.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

SCARA3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARA3	XM_017013536.3	c.1370-16339T>C		intron_variant
SCARA3	XM_017013537.2	c.1370-16339T>C		intron_variant
SCARA3	XR_949419.3	n.1773+5180T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90350 AN: 152006 Hom.: 27954 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.587

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.594 AC: 90383 AN: 152122 Hom.: 27948 Cov.: 33 AF XY: 0.595 AC XY: 44237 AN XY: 74362

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.590

Alfa AF: 0.663 Hom.: 56256

Bravo AF: 0.578

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.64
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs559251; hg19: chr8-27539370;