rs62322744

Positions:

• chr4-122529774-G-A
• chr4-122529774-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0491 in 152,220 control chromosomes in the GnomAD database, including 260 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 0.049 (260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0492 AC: 7485 AN: 152102 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0378

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0741

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0491 AC: 7477 AN: 152220 Hom.: 260 Cov.: 32 AF XY: 0.0498 AC XY: 3707 AN XY: 74420

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0378

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.0940

Gnomad4 NFE AF: 0.0741

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0367 Hom.: 36

Bravo AF: 0.0427

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62322744; hg19: chr4-123450929;