3-148556718-C-T

Variant names:

• chr3-148556718-C-T
• rs12490567
• ENST00000648979.2:n.116+35100G>A

Variant summary

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

The ENST00000648979.2(ENSG00000285557):​n.116+35100G>A 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 152,020 control chromosomes in the GnomAD database, including 40,457 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 (40457 hom., cov: 33)
• Consequence: ENSG00000285557 ENST00000648979.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 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+35100G>A		intron_variant	Intron 1 of 5
ENSG00000285557	ENST00000752703.1	n.118+35100G>A		intron_variant	Intron 1 of 6
ENSG00000285557	ENST00000752704.1	n.116+35100G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110862 AN: 151902 Hom.: 40415 Cov.: 33

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.730 AC: 110961 AN: 152020 Hom.: 40457 Cov.: 33 AF XY: 0.731 AC XY: 54365 AN XY: 74338

African (AFR) AF: 0.758 AC: 31445 AN: 41464

American (AMR) AF: 0.703 AC: 10721 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2554 AN: 3464

East Asian (EAS) AF: 0.728 AC: 3764 AN: 5168

South Asian (SAS) AF: 0.793 AC: 3826 AN: 4822

European-Finnish (FIN) AF: 0.736 AC: 7789 AN: 10584

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

European-Non Finnish (NFE) AF: 0.712 AC: 48387 AN: 67950

Other (OTH) AF: 0.736 AC: 1553 AN: 2110

Alfa AF: 0.719 Hom.: 5527

Bravo AF: 0.726

Asia WGS AF: 0.746 AC: 2592 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.6
DANN	Benign	0.17
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12490567; hg19: chr3-148274505;