1-172644101-A-G

Variant names:

• chr1-172644101-A-G
• rs2859228

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 0.459 in 151,788 control chromosomes in the GnomAD database, including 16,238 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 0.46 (16238 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.566 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: 0.459 AC: 69652 AN: 151670 Hom.: 16214 Cov.: 30

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.459 AC: 69717 AN: 151788 Hom.: 16238 Cov.: 30 AF XY: 0.462 AC XY: 34273 AN XY: 74186

African (AFR) AF: 0.444 AC: 18334 AN: 41328

American (AMR) AF: 0.403 AC: 6159 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1608 AN: 5148

South Asian (SAS) AF: 0.584 AC: 2812 AN: 4812

European-Finnish (FIN) AF: 0.509 AC: 5366 AN: 10532

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32210 AN: 67916

Other (OTH) AF: 0.458 AC: 967 AN: 2110

Alfa AF: 0.466 Hom.: 72131

Bravo AF: 0.443

Asia WGS AF: 0.472 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.51
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2859228; hg19: chr1-172613241;