rs2709984

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.877

Alfa AF: 0.877 Hom.: 44602

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2709984; hg19: chr7-137812369;