rs4964770

Variant names:

• chr12-108901732-T-C
• rs4964770

Your query was ambiguous. Multiple possible variants found:

• chr12-108901732-T-C
• chr12-108901732-T-G

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 0.345 in 151,870 control chromosomes in the GnomAD database, including 9,680 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 0.35 (9680 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 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: 0.345 AC: 52357 AN: 151752 Hom.: 9661 Cov.: 30

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.345 AC: 52437 AN: 151870 Hom.: 9680 Cov.: 30 AF XY: 0.354 AC XY: 26268 AN XY: 74232

African (AFR) AF: 0.400 AC: 16550 AN: 41390

American (AMR) AF: 0.508 AC: 7754 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1046 AN: 3468

East Asian (EAS) AF: 0.472 AC: 2432 AN: 5152

South Asian (SAS) AF: 0.381 AC: 1831 AN: 4802

European-Finnish (FIN) AF: 0.306 AC: 3233 AN: 10552

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18400 AN: 67944

Other (OTH) AF: 0.381 AC: 803 AN: 2106

Alfa AF: 0.303 Hom.: 17719

Bravo AF: 0.366

Asia WGS AF: 0.414 AC: 1441 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	0.59
DANN	Benign	0.35
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs4964770; hg19: chr12-109295508;