rs1595014

Variant names:

• chr7-12148903-T-A
• rs1595014

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 0.23 in 151,854 control chromosomes in the GnomAD database, including 4,354 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 0.23 (4354 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 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: 0.230 AC: 34886 AN: 151732 Hom.: 4354 Cov.: 30

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.230 AC: 34899 AN: 151854 Hom.: 4354 Cov.: 30 AF XY: 0.226 AC XY: 16780 AN XY: 74216

African (AFR) AF: 0.168 AC: 6979 AN: 41430

American (AMR) AF: 0.202 AC: 3070 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3472

East Asian (EAS) AF: 0.0597 AC: 307 AN: 5144

South Asian (SAS) AF: 0.163 AC: 781 AN: 4802

European-Finnish (FIN) AF: 0.278 AC: 2938 AN: 10570

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18991 AN: 67902

Other (OTH) AF: 0.245 AC: 516 AN: 2108

Alfa AF: 0.251 Hom.: 617

Bravo AF: 0.225

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.56
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1595014; hg19: chr7-12188529;