chr3-103105528-G-C

Position:

• chr3-103105528-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0758

Gnomad4 AMR AF: 0.0382

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.00522

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.0149

Gnomad4 NFE AF: 0.0341

Gnomad4 OTH AF: 0.0558

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511203; hg19: chr3-102824372;