chr3-148667378-G-C

Variant names:

• chr3-148667378-G-C
• rs275704

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 0.642 in 151,780 control chromosomes in the GnomAD database, including 35,692 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 0.64 (35692 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97437 AN: 151664 Hom.: 35682 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.642 AC: 97459 AN: 151780 Hom.: 35692 Cov.: 31 AF XY: 0.648 AC XY: 48066 AN XY: 74198

African (AFR) AF: 0.263 AC: 10858 AN: 41342

American (AMR) AF: 0.783 AC: 11934 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2774 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4603 AN: 5132

South Asian (SAS) AF: 0.640 AC: 3078 AN: 4806

European-Finnish (FIN) AF: 0.815 AC: 8583 AN: 10536

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53355 AN: 67946

Other (OTH) AF: 0.670 AC: 1405 AN: 2096

Alfa AF: 0.689 Hom.: 4688

Bravo AF: 0.629

Asia WGS AF: 0.714 AC: 2483 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.38
DANN	Benign	0.42
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs275704; hg19: chr3-148385165;