chr1-79533646-T-C

Variant names:

• chr1-79533646-T-C
• rs10493628

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 0.291 in 151,936 control chromosomes in the GnomAD database, including 8,153 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 0.29 (8153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 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: 0.291 AC: 44188 AN: 151818 Hom.: 8157 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.291 AC: 44165 AN: 151936 Hom.: 8153 Cov.: 32 AF XY: 0.288 AC XY: 21374 AN XY: 74268

African (AFR) AF: 0.0762 AC: 3167 AN: 41536

American (AMR) AF: 0.304 AC: 4627 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1579 AN: 3466

East Asian (EAS) AF: 0.177 AC: 914 AN: 5166

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4814

European-Finnish (FIN) AF: 0.357 AC: 3748 AN: 10502

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27388 AN: 67910

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.340 Hom.: 3222

Bravo AF: 0.280

Asia WGS AF: 0.202 AC: 698 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	16
DANN	Benign	0.84
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10493628; hg19: chr1-79999331;