rs1006514

Variant names:

• chr7-28921704-G-A
• rs1006514

Your query was ambiguous. Multiple possible variants found:

• chr7-28921704-G-A
• chr7-28921704-G-C

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 0.276 in 151,926 control chromosomes in the GnomAD database, including 6,585 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 0.28 (6585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.423 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: 0.275 AC: 41793 AN: 151808 Hom.: 6563 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.276 AC: 41866 AN: 151926 Hom.: 6585 Cov.: 32 AF XY: 0.273 AC XY: 20303 AN XY: 74246

African (AFR) AF: 0.428 AC: 17751 AN: 41434

American (AMR) AF: 0.248 AC: 3787 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3468

East Asian (EAS) AF: 0.0980 AC: 507 AN: 5176

South Asian (SAS) AF: 0.226 AC: 1091 AN: 4822

European-Finnish (FIN) AF: 0.243 AC: 2552 AN: 10508

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14704 AN: 67942

Other (OTH) AF: 0.249 AC: 525 AN: 2108

Alfa AF: 0.232 Hom.: 14108

Bravo AF: 0.283

Asia WGS AF: 0.216 AC: 748 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	0.10
DANN	Benign	0.42
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1006514; hg19: chr7-28961321;