7-116808996-T-C

Variant names:

• chr7-116808996-T-C
• rs41751

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 152,062 control chromosomes in the GnomAD database, including 10,376 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 (10376 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 52435 AN: 151944 Hom.: 10389 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.345 AC: 52401 AN: 152062 Hom.: 10376 Cov.: 32 AF XY: 0.350 AC XY: 26019 AN XY: 74328

African (AFR) AF: 0.136 AC: 5634 AN: 41514

American (AMR) AF: 0.416 AC: 6347 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1622 AN: 3472

East Asian (EAS) AF: 0.504 AC: 2605 AN: 5170

South Asian (SAS) AF: 0.484 AC: 2334 AN: 4820

European-Finnish (FIN) AF: 0.413 AC: 4362 AN: 10552

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28217 AN: 67956

Other (OTH) AF: 0.366 AC: 774 AN: 2112

Alfa AF: 0.366 Hom.: 1901

Bravo AF: 0.335

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.51
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs41751; hg19: chr7-116449050;