chr1-157467720-G-A

Variant names:

• chr1-157467720-G-A
• rs6686423

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 0.208 in 152,194 control chromosomes in the GnomAD database, including 4,144 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 0.21 (4144 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 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: 0.208 AC: 31670 AN: 152076 Hom.: 4147 Cov.: 33

Gnomad AFR AF: 0.0639

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.208 AC: 31673 AN: 152194 Hom.: 4144 Cov.: 33 AF XY: 0.207 AC XY: 15392 AN XY: 74402

African (AFR) AF: 0.0637 AC: 2646 AN: 41534

American (AMR) AF: 0.297 AC: 4544 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3472

East Asian (EAS) AF: 0.0933 AC: 484 AN: 5188

South Asian (SAS) AF: 0.0741 AC: 357 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2635 AN: 10570

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

European-Non Finnish (NFE) AF: 0.281 AC: 19128 AN: 68004

Other (OTH) AF: 0.226 AC: 477 AN: 2114

Alfa AF: 0.252 Hom.: 10046

Bravo AF: 0.206

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.80
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6686423; hg19: chr1-157437510;