1-79705683-C-T

Variant names:

• chr1-79705683-C-T
• rs7539480

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 0.148 in 152,084 control chromosomes in the GnomAD database, including 1,728 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 0.15 (1728 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.189 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: 0.148 AC: 22461 AN: 151972 Hom.: 1728 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.148 AC: 22479 AN: 152084 Hom.: 1728 Cov.: 33 AF XY: 0.146 AC XY: 10847 AN XY: 74342

African (AFR) AF: 0.159 AC: 6577 AN: 41458

American (AMR) AF: 0.113 AC: 1730 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3464

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5170

South Asian (SAS) AF: 0.200 AC: 962 AN: 4816

European-Finnish (FIN) AF: 0.113 AC: 1195 AN: 10592

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10061 AN: 67990

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.146 Hom.: 6283

Bravo AF: 0.147

Asia WGS AF: 0.198 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.50
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7539480; hg19: chr1-80171368;