1-163067527-G-A

Variant names:

• chr1-163067527-G-A
• rs6678136

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 0.433 in 151,992 control chromosomes in the GnomAD database, including 14,271 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 0.43 (14271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65736 AN: 151872 Hom.: 14256 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.433 AC: 65807 AN: 151992 Hom.: 14271 Cov.: 32 AF XY: 0.433 AC XY: 32169 AN XY: 74296

African (AFR) AF: 0.456 AC: 18912 AN: 41464

American (AMR) AF: 0.414 AC: 6326 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1371 AN: 3466

East Asian (EAS) AF: 0.436 AC: 2250 AN: 5164

South Asian (SAS) AF: 0.493 AC: 2376 AN: 4818

European-Finnish (FIN) AF: 0.379 AC: 4006 AN: 10572

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29112 AN: 67934

Other (OTH) AF: 0.446 AC: 941 AN: 2110

Alfa AF: 0.429 Hom.: 7319

Bravo AF: 0.433

Asia WGS AF: 0.489 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.54
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs6678136; hg19: chr1-163037317;