7-150984122-C-T

Variant names:

• chr7-150984122-C-T
• rs2373961

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 0.303 in 152,120 control chromosomes in the GnomAD database, including 7,641 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 0.30 (7641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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: 0.303 AC: 46129 AN: 152004 Hom.: 7639 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.303 AC: 46144 AN: 152120 Hom.: 7641 Cov.: 32 AF XY: 0.300 AC XY: 22295 AN XY: 74364

African (AFR) AF: 0.195 AC: 8073 AN: 41492

American (AMR) AF: 0.291 AC: 4452 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3470

East Asian (EAS) AF: 0.135 AC: 697 AN: 5180

South Asian (SAS) AF: 0.304 AC: 1464 AN: 4814

European-Finnish (FIN) AF: 0.353 AC: 3732 AN: 10582

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25530 AN: 67980

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.353 Hom.: 36579

Bravo AF: 0.294

Asia WGS AF: 0.223 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.2
DANN	Benign	0.81
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs2373961; hg19: chr7-150681210;