chr1-102873555-G-A

Variant names:

• chr1-102873555-G-A
• rs1241209

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 0.253 in 151,882 control chromosomes in the GnomAD database, including 5,245 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 0.25 (5245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 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: 0.253 AC: 38435 AN: 151760 Hom.: 5245 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.253 AC: 38457 AN: 151882 Hom.: 5245 Cov.: 32 AF XY: 0.251 AC XY: 18597 AN XY: 74212

African (AFR) AF: 0.334 AC: 13812 AN: 41412

American (AMR) AF: 0.219 AC: 3332 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1131 AN: 3464

East Asian (EAS) AF: 0.334 AC: 1717 AN: 5140

South Asian (SAS) AF: 0.348 AC: 1673 AN: 4810

European-Finnish (FIN) AF: 0.150 AC: 1580 AN: 10550

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14429 AN: 67948

Other (OTH) AF: 0.270 AC: 568 AN: 2104

Alfa AF: 0.223 Hom.: 474

Bravo AF: 0.258

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.22
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1241209; hg19: chr1-103339111;