chr1-29964421-A-G

Variant names:

• chr1-29964421-A-G
• rs6694545

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 0.587 in 151,906 control chromosomes in the GnomAD database, including 30,654 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 0.59 (30654 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 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: 0.588 AC: 89233 AN: 151788 Hom.: 30651 Cov.: 30

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.587 AC: 89242 AN: 151906 Hom.: 30654 Cov.: 30 AF XY: 0.589 AC XY: 43706 AN XY: 74220

African (AFR) AF: 0.207 AC: 8565 AN: 41432

American (AMR) AF: 0.627 AC: 9581 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2595 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3795 AN: 5128

South Asian (SAS) AF: 0.515 AC: 2463 AN: 4786

European-Finnish (FIN) AF: 0.784 AC: 8275 AN: 10560

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51766 AN: 67948

Other (OTH) AF: 0.632 AC: 1332 AN: 2108

Alfa AF: 0.702 Hom.: 105986

Bravo AF: 0.566

Asia WGS AF: 0.552 AC: 1923 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	0.27
DANN	Benign	0.34
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs6694545; hg19: chr1-30437268; COSMIC: COSV59934505;