3-103120223-C-G

Variant names:

• chr3-103120223-C-G
• rs4856121

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 0.533 in 151,968 control chromosomes in the GnomAD database, including 24,132 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 0.53 (24132 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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: 0.534 AC: 81031 AN: 151850 Hom.: 24121 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.533 AC: 81057 AN: 151968 Hom.: 24132 Cov.: 32 AF XY: 0.539 AC XY: 40018 AN XY: 74262

African (AFR) AF: 0.248 AC: 10285 AN: 41436

American (AMR) AF: 0.643 AC: 9800 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3913 AN: 5176

South Asian (SAS) AF: 0.704 AC: 3391 AN: 4818

European-Finnish (FIN) AF: 0.617 AC: 6510 AN: 10554

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.632 AC: 42927 AN: 67960

Other (OTH) AF: 0.561 AC: 1182 AN: 2108

Alfa AF: 0.461 Hom.: 1476

Bravo AF: 0.522

Asia WGS AF: 0.657 AC: 2281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs4856121; hg19: chr3-102839067;