rs7079291

Variant names:

• chr10-111123010-T-G
• rs7079291

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 0.126 in 152,208 control chromosomes in the GnomAD database, including 1,309 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 0.13 (1309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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: 0.126 AC: 19143 AN: 152090 Hom.: 1310 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.0533

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.126 AC: 19148 AN: 152208 Hom.: 1309 Cov.: 32 AF XY: 0.123 AC XY: 9152 AN XY: 74420

African (AFR) AF: 0.105 AC: 4354 AN: 41536

American (AMR) AF: 0.0995 AC: 1522 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3472

East Asian (EAS) AF: 0.0594 AC: 307 AN: 5170

South Asian (SAS) AF: 0.0529 AC: 255 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1491 AN: 10598

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10221 AN: 67996

Other (OTH) AF: 0.131 AC: 276 AN: 2114

Alfa AF: 0.140 Hom.: 1988

Bravo AF: 0.122

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7079291; hg19: chr10-112882768;