chr7-21984422-T-C

Variant names:

• chr7-21984422-T-C
• rs1175000

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.393

Alfa AF: 0.452 Hom.: 33217

Bravo AF: 0.382

Asia WGS AF: 0.438 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1175000; hg19: chr7-22024040;