4-162338949-A-T

Position:

• chr4-162338949-A-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 0.798 in 152,144 control chromosomes in the GnomAD database, including 48,582 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 0.80 (48582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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: 0.798 AC: 121325 AN: 152026 Hom.: 48547 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.798 AC: 121415 AN: 152144 Hom.: 48582 Cov.: 32 AF XY: 0.801 AC XY: 59588 AN XY: 74378

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.792

Alfa AF: 0.799 Hom.: 6051

Bravo AF: 0.799

Asia WGS AF: 0.869 AC: 3022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1868699; hg19: chr4-163260101;