7-22810714-C-T

Variant names:

• chr7-22810714-C-T
• rs1029741

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 0.67 in 152,074 control chromosomes in the GnomAD database, including 34,897 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 0.67 (34897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.862
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101727 AN: 151956 Hom.: 34857 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.670 AC: 101831 AN: 152074 Hom.: 34897 Cov.: 32 AF XY: 0.666 AC XY: 49532 AN XY: 74342

African (AFR) AF: 0.811 AC: 33660 AN: 41498

American (AMR) AF: 0.584 AC: 8933 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1935 AN: 3470

East Asian (EAS) AF: 0.833 AC: 4315 AN: 5180

South Asian (SAS) AF: 0.572 AC: 2761 AN: 4828

European-Finnish (FIN) AF: 0.599 AC: 6325 AN: 10564

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41653 AN: 67932

Other (OTH) AF: 0.648 AC: 1366 AN: 2108

Alfa AF: 0.617 Hom.: 52777

Bravo AF: 0.674

Asia WGS AF: 0.732 AC: 2543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.3
DANN	Benign	0.74
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs1029741; hg19: chr7-22850333;