1-79693536-A-C

Position:

• chr1-79693536-A-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 0.883 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;