1-79714204-G-T

Position:

• chr1-79714204-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 26 gene

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: 0.0143 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

Gnomad4 AFR AF: 0.00434

Gnomad4 AMR AF: 0.0117

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00724

Gnomad4 FIN AF: 0.00998

Gnomad4 NFE AF: 0.0239

Gnomad4 OTH AF: 0.0123

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524183; hg19: chr1-80179889;