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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.275 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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0980

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.249

Alfa AF: 0.217 Hom.: 7623

Bravo AF: 0.283

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1006514; hg19: chr7-28961321;