rs3762802

Positions:

• chr3-131503879-T-C

Variant summary

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

The ENST00000661875.1(ENSG00000248468):​n.132+1175T>C 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 0.14 in 152,284 control chromosomes in the GnomAD database, including 1,641 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 0.14 (1641 hom., cov: 33)
• Consequence: ENST00000661875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

Genes affected

(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 (SAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374114	XR_007096087.1	n.176+795T>C		intron_variant, non_coding_transcript_variant
LOC105374114	XR_924495.4	n.176+795T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661875.1	n.132+1175T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21374 AN: 152166 Hom.: 1638 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.140 AC: 21394 AN: 152284 Hom.: 1641 Cov.: 33 AF XY: 0.141 AC XY: 10463 AN XY: 74460

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0880

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.0635

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.135

Alfa AF: 0.140 Hom.: 328

Bravo AF: 0.131

Asia WGS AF: 0.150 AC: 524 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	3.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3762802; hg19: chr3-131222723;