chr1-163064626-G-A

Variant names:

• chr1-163064626-G-A
• rs6427711

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 0.242 in 151,860 control chromosomes in the GnomAD database, including 4,547 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 0.24 (4547 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 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: 0.242 AC: 36744 AN: 151740 Hom.: 4543 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.242 AC: 36773 AN: 151860 Hom.: 4547 Cov.: 31 AF XY: 0.245 AC XY: 18160 AN XY: 74196

African (AFR) AF: 0.224 AC: 9275 AN: 41432

American (AMR) AF: 0.231 AC: 3511 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3464

East Asian (EAS) AF: 0.359 AC: 1838 AN: 5122

South Asian (SAS) AF: 0.400 AC: 1919 AN: 4802

European-Finnish (FIN) AF: 0.212 AC: 2246 AN: 10574

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16519 AN: 67930

Other (OTH) AF: 0.254 AC: 536 AN: 2112

Alfa AF: 0.242 Hom.: 1559

Bravo AF: 0.240

Asia WGS AF: 0.371 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.72
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs6427711; hg19: chr1-163034416;