3-103105528-G-C

Variant names:

• chr3-103105528-G-C
• rs10511203

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 0.0461 in 152,190 control chromosomes in the GnomAD database, including 220 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 0.046 (220 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.56
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0736 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: 0.0461 AC: 7003 AN: 152072 Hom.: 219 Cov.: 32

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0383

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.0149

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0461 AC: 7014 AN: 152190 Hom.: 220 Cov.: 32 AF XY: 0.0461 AC XY: 3429 AN XY: 74414

African (AFR) AF: 0.0758 AC: 3146 AN: 41526

American (AMR) AF: 0.0382 AC: 584 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3472

East Asian (EAS) AF: 0.00522 AC: 27 AN: 5172

South Asian (SAS) AF: 0.0782 AC: 377 AN: 4818

European-Finnish (FIN) AF: 0.0149 AC: 158 AN: 10608

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0341 AC: 2320 AN: 67990

Other (OTH) AF: 0.0558 AC: 118 AN: 2114

Alfa AF: 0.00515 Hom.: 2

Bravo AF: 0.0479

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.35
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs10511203; hg19: chr3-102824372;