4-171212786-A-C

Variant names:

• chr4-171212786-A-C
• rs2332211

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 0.841 in 152,174 control chromosomes in the GnomAD database, including 54,112 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 0.84 (54112 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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: 0.841 AC: 127821 AN: 152056 Hom.: 54072 Cov.: 33

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.841 AC: 127919 AN: 152174 Hom.: 54112 Cov.: 33 AF XY: 0.846 AC XY: 62956 AN XY: 74384

African (AFR) AF: 0.753 AC: 31272 AN: 41512

American (AMR) AF: 0.899 AC: 13738 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3026 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4824 AN: 5174

South Asian (SAS) AF: 0.915 AC: 4414 AN: 4824

European-Finnish (FIN) AF: 0.910 AC: 9650 AN: 10606

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58227 AN: 67994

Other (OTH) AF: 0.855 AC: 1805 AN: 2110

Alfa AF: 0.855 Hom.: 28433

Bravo AF: 0.837

Asia WGS AF: 0.901 AC: 3133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.53
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2332211; hg19: chr4-172133937;