3-148582691-T-G

Variant names:

• chr3-148582691-T-G
• rs2639365
• ENST00000648979.2:n.116+9127A>C

Variant summary

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

The ENST00000648979.2(ENSG00000285557):​n.116+9127A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,002 control chromosomes in the GnomAD database, including 40,493 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 0.73 (40493 hom., cov: 32)
• Consequence: ENSG00000285557 ENST00000648979.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 1 publications found

Genes affected

ENSG00000285557 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285557	ENST00000648979.2	n.116+9127A>C		intron_variant	Intron 1 of 5
ENSG00000285557	ENST00000752703.1	n.118+9127A>C		intron_variant	Intron 1 of 6
ENSG00000285557	ENST00000752704.1	n.116+9127A>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110898 AN: 151884 Hom.: 40447 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.730 AC: 111002 AN: 152002 Hom.: 40493 Cov.: 32 AF XY: 0.732 AC XY: 54356 AN XY: 74278

African (AFR) AF: 0.760 AC: 31532 AN: 41496

American (AMR) AF: 0.703 AC: 10727 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2555 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3761 AN: 5160

South Asian (SAS) AF: 0.795 AC: 3827 AN: 4814

European-Finnish (FIN) AF: 0.736 AC: 7767 AN: 10554

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48355 AN: 67932

Other (OTH) AF: 0.737 AC: 1558 AN: 2114

Alfa AF: 0.712 Hom.: 6243

Bravo AF: 0.727

Asia WGS AF: 0.748 AC: 2598 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.1
DANN	Benign	0.76
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2639365; hg19: chr3-148300478;