chr13-30705122-C-T

Variant names:

• chr13-30705122-C-T
• rs7995384

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 0.582 in 152,116 control chromosomes in the GnomAD database, including 28,479 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 0.58 (28479 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 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: 0.582 AC: 88420 AN: 151998 Hom.: 28471 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.582 AC: 88471 AN: 152116 Hom.: 28479 Cov.: 33 AF XY: 0.581 AC XY: 43198 AN XY: 74388

African (AFR) AF: 0.286 AC: 11853 AN: 41470

American (AMR) AF: 0.613 AC: 9359 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2204 AN: 3470

East Asian (EAS) AF: 0.623 AC: 3229 AN: 5182

South Asian (SAS) AF: 0.476 AC: 2294 AN: 4822

European-Finnish (FIN) AF: 0.750 AC: 7934 AN: 10576

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49446 AN: 68000

Other (OTH) AF: 0.615 AC: 1299 AN: 2112

Alfa AF: 0.668 Hom.: 110352

Bravo AF: 0.560

Asia WGS AF: 0.494 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.058
DANN	Benign	0.83
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7995384; hg19: chr13-31279259;