chr1-79693536-A-C

Variant names:

• chr1-79693536-A-C
• rs1524174

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 0.883 in 152,148 control chromosomes in the GnomAD database, including 59,978 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 0.88 (59978 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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: 0.883 AC: 134273 AN: 152032 Hom.: 59942 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.883 AC: 134361 AN: 152148 Hom.: 59978 Cov.: 31 AF XY: 0.884 AC XY: 65736 AN XY: 74402

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.881

Alfa AF: 0.932 Hom.: 82592

Bravo AF: 0.875

Asia WGS AF: 0.888 AC: 3087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.6
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524174; hg19: chr1-80159221;