3-103588798-T-G

Variant names:

• chr3-103588798-T-G
• rs7612581

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 0.487 in 151,870 control chromosomes in the GnomAD database, including 21,662 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 0.49 (21662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73883 AN: 151752 Hom.: 21592 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.487 AC: 74025 AN: 151870 Hom.: 21662 Cov.: 32 AF XY: 0.495 AC XY: 36734 AN XY: 74218

African (AFR) AF: 0.817 AC: 33909 AN: 41492

American (AMR) AF: 0.483 AC: 7370 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1236 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2891 AN: 5160

South Asian (SAS) AF: 0.572 AC: 2759 AN: 4822

European-Finnish (FIN) AF: 0.382 AC: 4010 AN: 10498

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20475 AN: 67872

Other (OTH) AF: 0.485 AC: 1022 AN: 2108

Alfa AF: 0.359 Hom.: 39126

Bravo AF: 0.509

Asia WGS AF: 0.633 AC: 2194 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.73
DANN	Benign	0.77
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7612581; hg19: chr3-103307642;