chr7-116513961-T-G

Position:

• chr7-116513961-T-G

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 0.345 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.345 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

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.342

Alfa AF: 0.324 Hom.: 1282

Bravo AF: 0.351

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17588172; hg19: chr7-116154015;