7-150814835-C-T

Variant names:

• chr7-150814835-C-T
• rs1006581

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 0.53 in 151,926 control chromosomes in the GnomAD database, including 22,001 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 0.53 (22001 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 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: 0.530 AC: 80394 AN: 151808 Hom.: 21970 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.530 AC: 80475 AN: 151926 Hom.: 22001 Cov.: 31 AF XY: 0.533 AC XY: 39570 AN XY: 74234

African (AFR) AF: 0.621 AC: 25719 AN: 41436

American (AMR) AF: 0.517 AC: 7892 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3861 AN: 5148

South Asian (SAS) AF: 0.648 AC: 3116 AN: 4812

European-Finnish (FIN) AF: 0.474 AC: 4992 AN: 10542

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31466 AN: 67938

Other (OTH) AF: 0.529 AC: 1118 AN: 2112

Alfa AF: 0.501 Hom.: 5088

Bravo AF: 0.537

Asia WGS AF: 0.665 AC: 2306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.5
DANN	Benign	0.42
PhyloP100		-0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1006581;

hg19: chr7-150511923;