chr4-81299170-A-C

Variant names:

• chr4-81299170-A-C
• rs2011962

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 0.388 in 152,088 control chromosomes in the GnomAD database, including 14,571 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 0.39 (14571 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.387 AC: 58832 AN: 151968 Hom.: 14533 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.388 AC: 58937 AN: 152088 Hom.: 14571 Cov.: 33 AF XY: 0.379 AC XY: 28207 AN XY: 74338

African (AFR) AF: 0.709 AC: 29414 AN: 41496

American (AMR) AF: 0.306 AC: 4678 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 935 AN: 3470

East Asian (EAS) AF: 0.182 AC: 942 AN: 5170

South Asian (SAS) AF: 0.234 AC: 1130 AN: 4820

European-Finnish (FIN) AF: 0.233 AC: 2463 AN: 10574

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18336 AN: 67960

Other (OTH) AF: 0.337 AC: 711 AN: 2108

Alfa AF: 0.320 Hom.: 17882

Bravo AF: 0.408

Asia WGS AF: 0.225 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.24
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2011962; hg19: chr4-82220324;