1-194454817-G-A

Variant names:

• chr1-194454817-G-A
• rs6428237

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 0.577 in 151,908 control chromosomes in the GnomAD database, including 25,878 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 0.58 (25878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 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: 0.577 AC: 87608 AN: 151790 Hom.: 25887 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.577 AC: 87603 AN: 151908 Hom.: 25878 Cov.: 31 AF XY: 0.569 AC XY: 42255 AN XY: 74242

African (AFR) AF: 0.468 AC: 19387 AN: 41414

American (AMR) AF: 0.583 AC: 8900 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2262 AN: 3464

East Asian (EAS) AF: 0.686 AC: 3516 AN: 5128

South Asian (SAS) AF: 0.415 AC: 1999 AN: 4818

European-Finnish (FIN) AF: 0.527 AC: 5567 AN: 10558

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43845 AN: 67952

Other (OTH) AF: 0.626 AC: 1323 AN: 2112

Alfa AF: 0.581 Hom.: 4449

Bravo AF: 0.579

Asia WGS AF: 0.546 AC: 1898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.35
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6428237; hg19: chr1-194423947;