rs2708997

Variant names:

• chr7-9583663-T-C
• rs2708997

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 0.337 in 151,920 control chromosomes in the GnomAD database, including 9,516 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 0.34 (9516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 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: 0.337 AC: 51121 AN: 151802 Hom.: 9507 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.337 AC: 51145 AN: 151920 Hom.: 9516 Cov.: 32 AF XY: 0.336 AC XY: 24965 AN XY: 74246

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.353

Alfa AF: 0.388 Hom.: 5468

Bravo AF: 0.334

Asia WGS AF: 0.261 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2708997; hg19: chr7-9623293;