chr7-152678103-T-C

Variant names:

• chr7-152678103-T-C
• rs2040639

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 0.62 in 151,986 control chromosomes in the GnomAD database, including 30,861 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 0.62 (30861 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 24 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 (AFR) allele frequency at 95% confidence interval = 0.825 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: 0.620 AC: 94132 AN: 151868 Hom.: 30814 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.620 AC: 94238 AN: 151986 Hom.: 30861 Cov.: 32 AF XY: 0.614 AC XY: 45590 AN XY: 74276

African (AFR) AF: 0.833 AC: 34546 AN: 41494

American (AMR) AF: 0.616 AC: 9381 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2045 AN: 3464

East Asian (EAS) AF: 0.573 AC: 2952 AN: 5156

South Asian (SAS) AF: 0.645 AC: 3105 AN: 4812

European-Finnish (FIN) AF: 0.386 AC: 4078 AN: 10552

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

European-Non Finnish (NFE) AF: 0.535 AC: 36347 AN: 67958

Other (OTH) AF: 0.611 AC: 1285 AN: 2104

Alfa AF: 0.574 Hom.: 66586

Bravo AF: 0.644

Asia WGS AF: 0.629 AC: 2185 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	4.4
DANN	Benign	0.52
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2040639; hg19: chr7-152375188;