rs2196712

Variant names:

• chr4-117151133-G-A
• rs2196712

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 0.454 in 152,086 control chromosomes in the GnomAD database, including 16,095 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 0.45 (16095 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.521 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: 0.454 AC: 68935 AN: 151968 Hom.: 16081 Cov.: 33

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.454 AC: 68987 AN: 152086 Hom.: 16095 Cov.: 33 AF XY: 0.452 AC XY: 33621 AN XY: 74346

African (AFR) AF: 0.341 AC: 14148 AN: 41498

American (AMR) AF: 0.531 AC: 8109 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3472

East Asian (EAS) AF: 0.406 AC: 2092 AN: 5148

South Asian (SAS) AF: 0.461 AC: 2226 AN: 4824

European-Finnish (FIN) AF: 0.501 AC: 5301 AN: 10572

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34150 AN: 67976

Other (OTH) AF: 0.480 AC: 1014 AN: 2112

Alfa AF: 0.494 Hom.: 33878

Bravo AF: 0.452

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.31
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2196712; hg19: chr4-118072289;