1-157160775-A-G

Variant names:

• chr1-157160775-A-G
• rs6427356

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 0.348 in 151,996 control chromosomes in the GnomAD database, including 10,394 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 0.35 (10394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.348 AC: 52816 AN: 151878 Hom.: 10357 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.348 AC: 52904 AN: 151996 Hom.: 10394 Cov.: 32 AF XY: 0.355 AC XY: 26418 AN XY: 74318

African (AFR) AF: 0.358 AC: 14843 AN: 41418

American (AMR) AF: 0.473 AC: 7219 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4304 AN: 5182

South Asian (SAS) AF: 0.572 AC: 2758 AN: 4820

European-Finnish (FIN) AF: 0.284 AC: 3006 AN: 10574

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18852 AN: 67950

Other (OTH) AF: 0.357 AC: 753 AN: 2110

Alfa AF: 0.320 Hom.: 16126

Bravo AF: 0.360

Asia WGS AF: 0.685 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.7
DANN	Benign	0.81
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6427356; hg19: chr1-157130566;