chr1-79533646-T-C

Position:

• chr1-79533646-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.335

Alfa AF: 0.345 Hom.: 1671

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493628; hg19: chr1-79999331;