7-21984422-T-C

Variant names:

• chr7-21984422-T-C
• rs1175000

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 0.401 in 152,092 control chromosomes in the GnomAD database, including 12,999 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 0.40 (12999 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 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: 0.401 AC: 60910 AN: 151974 Hom.: 12986 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.401 AC: 60949 AN: 152092 Hom.: 12999 Cov.: 33 AF XY: 0.404 AC XY: 30037 AN XY: 74362

African (AFR) AF: 0.261 AC: 10848 AN: 41484

American (AMR) AF: 0.385 AC: 5875 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1469 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2425 AN: 5172

South Asian (SAS) AF: 0.480 AC: 2317 AN: 4826

European-Finnish (FIN) AF: 0.510 AC: 5394 AN: 10576

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31350 AN: 67978

Other (OTH) AF: 0.393 AC: 829 AN: 2108

Alfa AF: 0.438 Hom.: 45178

Bravo AF: 0.382

Asia WGS AF: 0.438 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1175000; hg19: chr7-22024040;