rs2709984

Variant names:

• chr7-138127623-C-A
• rs2709984

Your query was ambiguous. Multiple possible variants found:

• chr7-138127623-C-A
• chr7-138127623-C-T

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 0.887 in 152,202 control chromosomes in the GnomAD database, including 60,288 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 0.89 (60288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 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: 0.887 AC: 134901 AN: 152084 Hom.: 60237 Cov.: 32

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.887 AC: 135010 AN: 152202 Hom.: 60288 Cov.: 32 AF XY: 0.881 AC XY: 65558 AN XY: 74390

African (AFR) AF: 0.971 AC: 40361 AN: 41570

American (AMR) AF: 0.776 AC: 11856 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3186 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4433 AN: 5160

South Asian (SAS) AF: 0.961 AC: 4639 AN: 4826

European-Finnish (FIN) AF: 0.765 AC: 8089 AN: 10578

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59527 AN: 68006

Other (OTH) AF: 0.877 AC: 1855 AN: 2114

Alfa AF: 0.880 Hom.: 68039

Bravo AF: 0.887

Asia WGS AF: 0.924 AC: 3215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.70
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2709984; hg19: chr7-137812369;