1-79714204-G-C

Variant names:

• chr1-79714204-G-C
• rs1524183

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 0.781 in 152,136 control chromosomes in the GnomAD database, including 48,706 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 0.78 (48706 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.9 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: 0.781 AC: 118747 AN: 152018 Hom.: 48706 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.781 AC: 118773 AN: 152136 Hom.: 48706 Cov.: 33 AF XY: 0.781 AC XY: 58086 AN XY: 74390

African (AFR) AF: 0.509 AC: 21083 AN: 41450

American (AMR) AF: 0.858 AC: 13115 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3230 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3569 AN: 5162

South Asian (SAS) AF: 0.788 AC: 3805 AN: 4826

European-Finnish (FIN) AF: 0.914 AC: 9701 AN: 10614

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61595 AN: 68020

Other (OTH) AF: 0.784 AC: 1651 AN: 2106

Alfa AF: 0.814 Hom.: 2758

Bravo AF: 0.779

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs1524183; hg19: chr1-80179889;