3-103495441-G-C

Variant names:

• chr3-103495441-G-C
• rs10511212

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 0.0277 in 152,110 control chromosomes in the GnomAD database, including 131 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 0.028 (131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 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: 0.0277 AC: 4206 AN: 151992 Hom.: 131 Cov.: 32

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00934

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00901

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0277 AC: 4209 AN: 152110 Hom.: 131 Cov.: 32 AF XY: 0.0302 AC XY: 2244 AN XY: 74352

African (AFR) AF: 0.0363 AC: 1505 AN: 41488

American (AMR) AF: 0.0587 AC: 894 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3472

East Asian (EAS) AF: 0.107 AC: 555 AN: 5170

South Asian (SAS) AF: 0.101 AC: 486 AN: 4818

European-Finnish (FIN) AF: 0.00934 AC: 99 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00901 AC: 613 AN: 68002

Other (OTH) AF: 0.0175 AC: 37 AN: 2110

Alfa AF: 0.00466 Hom.: 2

Bravo AF: 0.0306

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.2
DANN	Benign	0.44
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs10511212; hg19: chr3-103214285;