chr1-153783607-G-A

Variant names:

• chr1-153783607-G-A
• rs6665637

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 151,530 control chromosomes in the GnomAD database, including 4,754 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 (4754 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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: 36670 AN: 151412 Hom.: 4754 Cov.: 30

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0176

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.242 AC: 36679 AN: 151530 Hom.: 4754 Cov.: 30 AF XY: 0.235 AC XY: 17376 AN XY: 74062

African (AFR) AF: 0.242 AC: 9975 AN: 41270

American (AMR) AF: 0.197 AC: 3001 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1098 AN: 3460

East Asian (EAS) AF: 0.0174 AC: 90 AN: 5172

South Asian (SAS) AF: 0.130 AC: 625 AN: 4810

European-Finnish (FIN) AF: 0.218 AC: 2285 AN: 10476

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18806 AN: 67768

Other (OTH) AF: 0.242 AC: 510 AN: 2106

Alfa AF: 0.251 Hom.: 5716

Bravo AF: 0.237

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.7
DANN	Benign	0.76
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6665637; hg19: chr1-153756083;