4-162338949-A-T

Variant names:

• chr4-162338949-A-T
• rs1868699

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;