rs62323881

Variant names:

• chr4-122117140-C-A
• rs62323881

Your query was ambiguous. Multiple possible variants found:

• chr4-122117140-C-A
• chr4-122117140-C-T

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 0.0502 in 152,234 control chromosomes in the GnomAD database, including 282 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 0.050 (282 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0731 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: 0.0503 AC: 7648 AN: 152116 Hom.: 282 Cov.: 31

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0967

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.0463

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

GnomAD4 genome AF: 0.0502 AC: 7639 AN: 152234 Hom.: 282 Cov.: 31 AF XY: 0.0511 AC XY: 3802 AN XY: 74426

African (AFR) AF: 0.0105 AC: 437 AN: 41548

American (AMR) AF: 0.0404 AC: 618 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4816

European-Finnish (FIN) AF: 0.0967 AC: 1024 AN: 10592

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0748 AC: 5086 AN: 68010

Other (OTH) AF: 0.0449 AC: 95 AN: 2116

Alfa AF: 0.0346 Hom.: 62

Bravo AF: 0.0437

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.69
DANN	Benign	0.75
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs62323881; hg19: chr4-123038295;