1-235547272-G-A

Variant names:

• chr1-235547272-G-A
• rs6664219

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 0.567 in 151,914 control chromosomes in the GnomAD database, including 25,023 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 0.57 (25023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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: 0.567 AC: 86055 AN: 151794 Hom.: 25010 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.567 AC: 86111 AN: 151914 Hom.: 25023 Cov.: 31 AF XY: 0.570 AC XY: 42315 AN XY: 74248

African (AFR) AF: 0.491 AC: 20342 AN: 41434

American (AMR) AF: 0.619 AC: 9467 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3472

East Asian (EAS) AF: 0.830 AC: 4264 AN: 5140

South Asian (SAS) AF: 0.498 AC: 2396 AN: 4812

European-Finnish (FIN) AF: 0.614 AC: 6496 AN: 10572

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39135 AN: 67890

Other (OTH) AF: 0.597 AC: 1260 AN: 2112

Alfa AF: 0.581 Hom.: 9833

Bravo AF: 0.567

Asia WGS AF: 0.650 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.31
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs6664219; hg19: chr1-235710572; COSMIC: COSV63999086;