1-162024220-G-T

Variant names:

• chr1-162024220-G-T
• rs4657136

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 0.533 in 151,620 control chromosomes in the GnomAD database, including 26,438 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 0.53 (26438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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: 0.533 AC: 80768 AN: 151500 Hom.: 26433 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.533 AC: 80779 AN: 151620 Hom.: 26438 Cov.: 32 AF XY: 0.535 AC XY: 39697 AN XY: 74142

African (AFR) AF: 0.136 AC: 5651 AN: 41410

American (AMR) AF: 0.680 AC: 10355 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2198 AN: 3438

East Asian (EAS) AF: 0.411 AC: 2120 AN: 5154

South Asian (SAS) AF: 0.482 AC: 2323 AN: 4820

European-Finnish (FIN) AF: 0.718 AC: 7583 AN: 10564

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48385 AN: 67706

Other (OTH) AF: 0.560 AC: 1178 AN: 2102

Alfa AF: 0.585 Hom.: 3832

Bravo AF: 0.514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.30
DANN	Benign	0.54
PhyloP100		-3.0
PromoterAI		0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4657136; hg19: chr1-161994010;