7-107854772-T-C

Variant names:

• chr7-107854772-T-C
• rs6949033

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 0.54 in 151,952 control chromosomes in the GnomAD database, including 23,369 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 0.54 (23369 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 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: 0.540 AC: 81997 AN: 151836 Hom.: 23362 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.540 AC: 82020 AN: 151952 Hom.: 23369 Cov.: 31 AF XY: 0.547 AC XY: 40606 AN XY: 74278

African (AFR) AF: 0.349 AC: 14474 AN: 41424

American (AMR) AF: 0.607 AC: 9263 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2188 AN: 3472

East Asian (EAS) AF: 0.790 AC: 4074 AN: 5154

South Asian (SAS) AF: 0.548 AC: 2636 AN: 4812

European-Finnish (FIN) AF: 0.622 AC: 6571 AN: 10570

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40801 AN: 67956

Other (OTH) AF: 0.573 AC: 1207 AN: 2106

Alfa AF: 0.565 Hom.: 9652

Bravo AF: 0.529

Asia WGS AF: 0.693 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.46
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6949033; hg19: chr7-107495217;