rs4964684

Variant names:

• chr12-108382643-G-T
• rs4964684

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 0.101 in 152,024 control chromosomes in the GnomAD database, including 1,995 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 0.10 (1995 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.101 AC: 15295 AN: 151906 Hom.: 1981 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.0747

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.000850

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00257

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.101 AC: 15355 AN: 152024 Hom.: 1995 Cov.: 32 AF XY: 0.101 AC XY: 7483 AN XY: 74332

African (AFR) AF: 0.265 AC: 10988 AN: 41410

American (AMR) AF: 0.232 AC: 3539 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.000577 AC: 2 AN: 3468

East Asian (EAS) AF: 0.0749 AC: 387 AN: 5170

South Asian (SAS) AF: 0.0127 AC: 61 AN: 4816

European-Finnish (FIN) AF: 0.000850 AC: 9 AN: 10586

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00257 AC: 175 AN: 67998

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0379 Hom.: 1955

Bravo AF: 0.130

Asia WGS AF: 0.0560 AC: 195 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.77
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4964684; hg19: chr12-108776420;