3-148697390-T-C

Variant names:

• chr3-148697390-T-C
• rs1492078

Variant summary

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

The variant allele was found at a frequency of 0.515 in 152,048 control chromosomes in the GnomAD database, including 23,991 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 0.51 (23991 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78233 AN: 151930 Hom.: 23980 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.515 AC: 78249 AN: 152048 Hom.: 23991 Cov.: 31 AF XY: 0.521 AC XY: 38759 AN XY: 74328

African (AFR) AF: 0.163 AC: 6751 AN: 41504

American (AMR) AF: 0.670 AC: 10235 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3470

East Asian (EAS) AF: 0.812 AC: 4200 AN: 5170

South Asian (SAS) AF: 0.586 AC: 2826 AN: 4824

European-Finnish (FIN) AF: 0.684 AC: 7216 AN: 10556

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43229 AN: 67940

Other (OTH) AF: 0.524 AC: 1101 AN: 2102

Alfa AF: 0.587 Hom.: 10955

Bravo AF: 0.503

Asia WGS AF: 0.660 AC: 2293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		-0.51
PromoterAI		-0.013	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1492078; hg19: chr3-148415177;