chr3-131503879-T-C

Variant names:

• chr3-131503879-T-C
• rs3762802
• ENST00000655300.1:n.117+1175T>C

Variant summary

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

The ENST00000655300.1(ENSG00000248468):​n.117+1175T>C variant causes a intron 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: ENSG00000248468 ENST00000655300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 2 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=-0.82).
• 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 rank	MANE	Protein	UniProt
LOC105374114	NR_189110.1	n.106+1175T>C		intron_variant	Intron 1 of 3
LOC105374114	NR_189111.1	n.106+1175T>C		intron_variant	Intron 1 of 2
LOC105374114	NR_189112.1	n.94+877T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248468	ENST00000655300.1	n.117+1175T>C		intron_variant	Intron 1 of 3
ENSG00000248468	ENST00000655982.1	n.55+781T>C		intron_variant	Intron 1 of 2
ENSG00000248468	ENST00000660541.1	n.146+785T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.110 AC: 4571 AN: 41568

American (AMR) AF: 0.0880 AC: 1347 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3470

East Asian (EAS) AF: 0.0635 AC: 330 AN: 5194

South Asian (SAS) AF: 0.199 AC: 958 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1725 AN: 10600

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11095 AN: 68008

Other (OTH) AF: 0.135 AC: 286 AN: 2112

Alfa AF: 0.139 Hom.: 332

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
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs3762802; hg19: chr3-131222723;