rs1005256

Variant names:

• chr7-14999980-C-A
• rs1005256

Your query was ambiguous. Multiple possible variants found:

• chr7-14999980-C-A
• chr7-14999980-C-G
• chr7-14999980-C-T

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 0.634 in 151,950 control chromosomes in the GnomAD database, including 30,904 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 0.63 (30904 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 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: 0.634 AC: 96299 AN: 151834 Hom.: 30890 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.634 AC: 96368 AN: 151950 Hom.: 30904 Cov.: 33 AF XY: 0.637 AC XY: 47292 AN XY: 74256

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.621

Alfa AF: 0.588 Hom.: 11386

Bravo AF: 0.636

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1005256; hg19: chr7-15039605;