7-80980631-C-A

Variant names:

• chr7-80980631-C-A
• rs2367090

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 0.203 in 152,020 control chromosomes in the GnomAD database, including 3,741 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 0.20 (3741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 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: 0.204 AC: 30915 AN: 151902 Hom.: 3743 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.203 AC: 30924 AN: 152020 Hom.: 3741 Cov.: 32 AF XY: 0.207 AC XY: 15378 AN XY: 74268

African (AFR) AF: 0.0805 AC: 3343 AN: 41520

American (AMR) AF: 0.224 AC: 3420 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3472

East Asian (EAS) AF: 0.175 AC: 903 AN: 5152

South Asian (SAS) AF: 0.206 AC: 995 AN: 4826

European-Finnish (FIN) AF: 0.344 AC: 3613 AN: 10516

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17332 AN: 67960

Other (OTH) AF: 0.190 AC: 400 AN: 2110

Alfa AF: 0.240 Hom.: 2620

Bravo AF: 0.187

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.74
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2367090; hg19: chr7-80609947;