chr1-221649561-A-G

Variant names:

• chr1-221649561-A-G
• rs10495174

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 0.358 in 152,016 control chromosomes in the GnomAD database, including 9,929 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 0.36 (9929 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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: 0.358 AC: 54347 AN: 151898 Hom.: 9922 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.358 AC: 54394 AN: 152016 Hom.: 9929 Cov.: 33 AF XY: 0.353 AC XY: 26238 AN XY: 74336

African (AFR) AF: 0.413 AC: 17132 AN: 41482

American (AMR) AF: 0.353 AC: 5386 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1178 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1453 AN: 5170

South Asian (SAS) AF: 0.287 AC: 1387 AN: 4826

European-Finnish (FIN) AF: 0.285 AC: 3010 AN: 10556

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23682 AN: 67934

Other (OTH) AF: 0.388 AC: 819 AN: 2110

Alfa AF: 0.359 Hom.: 5116

Bravo AF: 0.368

Asia WGS AF: 0.324 AC: 1124 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.2
DANN	Benign	0.74
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10495174; hg19: chr1-221822903; COSMIC: COSV60032339;