rs55867206

Positions:

• chr5-172492650-C-T

Variant summary

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

The ENST00000660356.1(ENSG00000287814):​n.331+13046C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,206 control chromosomes in the GnomAD database, including 660 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 0.083 (660 hom., cov: 32)
• Consequence: ENST00000660356.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377727	XR_941225.3	n.554+13046C>T		intron_variant, non_coding_transcript_variant
LOC105377727	XR_001742994.2	n.522+12517C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000660356.1	n.331+13046C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12668 AN: 152086 Hom.: 662 Cov.: 32

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0765

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0832 AC: 12657 AN: 152206 Hom.: 660 Cov.: 32 AF XY: 0.0838 AC XY: 6234 AN XY: 74428

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.0614

Gnomad4 ASJ AF: 0.0765

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0913

Alfa AF: 0.101 Hom.: 114

Bravo AF: 0.0726

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55867206; hg19: chr5-171919654;