rs1530947

Variant names:

• chr14-49484632-T-C
• rs1530947

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 0.169 in 152,190 control chromosomes in the GnomAD database, including 2,350 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 0.17 (2350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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: 0.169 AC: 25763 AN: 152072 Hom.: 2354 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.00711

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.169 AC: 25771 AN: 152190 Hom.: 2350 Cov.: 32 AF XY: 0.167 AC XY: 12436 AN XY: 74412

African (AFR) AF: 0.165 AC: 6843 AN: 41544

American (AMR) AF: 0.129 AC: 1978 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3470

East Asian (EAS) AF: 0.00713 AC: 37 AN: 5190

South Asian (SAS) AF: 0.0849 AC: 410 AN: 4828

European-Finnish (FIN) AF: 0.192 AC: 2028 AN: 10588

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

European-Non Finnish (NFE) AF: 0.194 AC: 13180 AN: 67968

Other (OTH) AF: 0.174 AC: 368 AN: 2112

Alfa AF: 0.188 Hom.: 12026

Bravo AF: 0.166

Asia WGS AF: 0.0660 AC: 233 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.046
DANN	Benign	0.56
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1530947; hg19: chr14-49951350;