7-116513961-T-G

Variant names:

• chr7-116513961-T-G
• rs17588172

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 0.345 in 151,936 control chromosomes in the GnomAD database, including 9,318 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 0.35 (9318 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52437 AN: 151818 Hom.: 9315 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.345 AC: 52465 AN: 151936 Hom.: 9318 Cov.: 31 AF XY: 0.341 AC XY: 25288 AN XY: 74240

African (AFR) AF: 0.398 AC: 16474 AN: 41414

American (AMR) AF: 0.304 AC: 4653 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1333 AN: 3464

East Asian (EAS) AF: 0.174 AC: 898 AN: 5172

South Asian (SAS) AF: 0.315 AC: 1511 AN: 4800

European-Finnish (FIN) AF: 0.313 AC: 3300 AN: 10538

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23099 AN: 67950

Other (OTH) AF: 0.342 AC: 721 AN: 2110

Alfa AF: 0.326 Hom.: 1345

Bravo AF: 0.351

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.59
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17588172;

hg19: chr7-116154015;