1-79714204-G-T

Variant names:

• chr1-79714204-G-T
• rs1524183

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0143 in 152,180 control chromosomes in the GnomAD database, including 26 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 0.014 (26 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).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0143 (2182/152180) while in subpopulation NFE AF = 0.0239 (1623/68020). AF 95% confidence interval is 0.0229. There are 26 homozygotes in GnomAd4. There are 1006 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 26 gene

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: 0.0143 AC: 2182 AN: 152062 Hom.: 26 Cov.: 33

Gnomad AFR AF: 0.00435

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0117

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00682

Gnomad FIN AF: 0.00998

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0239

Gnomad OTH AF: 0.0125

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

GnomAD4 genome AF: 0.0143 AC: 2182 AN: 152180 Hom.: 26 Cov.: 33 AF XY: 0.0135 AC XY: 1006 AN XY: 74418

African (AFR) AF: 0.00434 AC: 180 AN: 41466

American (AMR) AF: 0.0117 AC: 179 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.00724 AC: 35 AN: 4832

European-Finnish (FIN) AF: 0.00998 AC: 106 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0239 AC: 1623 AN: 68020

Other (OTH) AF: 0.0123 AC: 26 AN: 2106

Alfa AF: 0.0171 Hom.: 2758

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	0.37
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;