7-80970041-A-G

Variant names:

• chr7-80970041-A-G
• rs4236644

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 0.674 in 151,890 control chromosomes in the GnomAD database, including 35,589 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 0.67 (35589 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.763 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: 0.675 AC: 102380 AN: 151772 Hom.: 35563 Cov.: 30

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.674 AC: 102449 AN: 151890 Hom.: 35589 Cov.: 30 AF XY: 0.674 AC XY: 50033 AN XY: 74234

African (AFR) AF: 0.499 AC: 20649 AN: 41370

American (AMR) AF: 0.774 AC: 11815 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2542 AN: 3468

East Asian (EAS) AF: 0.579 AC: 2974 AN: 5140

South Asian (SAS) AF: 0.727 AC: 3494 AN: 4808

European-Finnish (FIN) AF: 0.736 AC: 7779 AN: 10564

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50797 AN: 67966

Other (OTH) AF: 0.694 AC: 1467 AN: 2114

Alfa AF: 0.722 Hom.: 136531

Bravo AF: 0.667

Asia WGS AF: 0.659 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.57
DANN	Benign	0.75
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs4236644; hg19: chr7-80599357;