7-116514777-G-T

Variant names:

• chr7-116514777-G-T
• rs6969706

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 0.267 in 151,958 control chromosomes in the GnomAD database, including 6,030 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 0.27 (6030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40580 AN: 151840 Hom.: 6028 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.267 AC: 40608 AN: 151958 Hom.: 6030 Cov.: 31 AF XY: 0.258 AC XY: 19127 AN XY: 74272

African (AFR) AF: 0.368 AC: 15257 AN: 41404

American (AMR) AF: 0.211 AC: 3215 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3470

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5180

South Asian (SAS) AF: 0.200 AC: 964 AN: 4828

European-Finnish (FIN) AF: 0.136 AC: 1436 AN: 10570

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17514 AN: 67940

Other (OTH) AF: 0.272 AC: 571 AN: 2102

Alfa AF: 0.232 Hom.: 1642

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.49
DANN	Benign	0.85
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs6969706; hg19: chr7-116154831;