3-131503741-C-T

Variant names:

• chr3-131503741-C-T
• rs3762803
• ENST00000655300.1:n.117+1037C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655300.1(ENSG00000248468):​n.117+1037C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,146 control chromosomes in the GnomAD database, including 42,815 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 0.74 (42815 hom., cov: 32)
• Consequence: ENSG00000248468 ENST00000655300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 1 publications found

Genes affected

ENSG00000248468 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374114	NR_189110.1	n.106+1037C>T		intron_variant	Intron 1 of 3
LOC105374114	NR_189111.1	n.106+1037C>T		intron_variant	Intron 1 of 2
LOC105374114	NR_189112.1	n.94+739C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248468	ENST00000655300.1	n.117+1037C>T		intron_variant	Intron 1 of 3
ENSG00000248468	ENST00000655982.1	n.55+643C>T		intron_variant	Intron 1 of 2
ENSG00000248468	ENST00000660541.1	n.146+647C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112353 AN: 152026 Hom.: 42758 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.739 AC: 112460 AN: 152146 Hom.: 42815 Cov.: 32 AF XY: 0.731 AC XY: 54382 AN XY: 74380

African (AFR) AF: 0.904 AC: 37535 AN: 41524

American (AMR) AF: 0.613 AC: 9366 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3472

East Asian (EAS) AF: 0.364 AC: 1883 AN: 5168

South Asian (SAS) AF: 0.618 AC: 2974 AN: 4816

European-Finnish (FIN) AF: 0.667 AC: 7056 AN: 10572

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48462 AN: 67998

Other (OTH) AF: 0.742 AC: 1569 AN: 2114

Alfa AF: 0.640 Hom.: 1969

Bravo AF: 0.738

Asia WGS AF: 0.546 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs3762803; hg19: chr3-131222585;