chr1-147004967-G-A

Variant names:

• chr1-147004967-G-A
• rs6656361

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 0.0806 in 152,056 control chromosomes in the GnomAD database, including 651 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 0.081 (651 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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: 0.0807 AC: 12267 AN: 151938 Hom.: 651 Cov.: 31

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0724

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0723

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0806 AC: 12258 AN: 152056 Hom.: 651 Cov.: 31 AF XY: 0.0827 AC XY: 6146 AN XY: 74336

African (AFR) AF: 0.0587 AC: 2432 AN: 41424

American (AMR) AF: 0.128 AC: 1951 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0724 AC: 251 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5168

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4828

European-Finnish (FIN) AF: 0.113 AC: 1197 AN: 10564

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0723 AC: 4918 AN: 68002

Other (OTH) AF: 0.0682 AC: 144 AN: 2110

Alfa AF: 0.0630 Hom.: 153

Bravo AF: 0.0801

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.060
DANN	Benign	0.38
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6656361; hg19: chr1-146476526;