rs1950712

Variant names:

• chr14-69013847-A-G
• rs1950712

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 0.0513 in 152,158 control chromosomes in the GnomAD database, including 302 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 0.051 (302 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0777 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: 0.0514 AC: 7811 AN: 152040 Hom.: 302 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.0246

Gnomad EAS AF: 0.00850

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0513 AC: 7812 AN: 152158 Hom.: 302 Cov.: 32 AF XY: 0.0508 AC XY: 3781 AN XY: 74374

African (AFR) AF: 0.0124 AC: 514 AN: 41534

American (AMR) AF: 0.0339 AC: 519 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0246 AC: 85 AN: 3462

East Asian (EAS) AF: 0.00852 AC: 44 AN: 5162

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4810

European-Finnish (FIN) AF: 0.0982 AC: 1041 AN: 10596

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0795 AC: 5406 AN: 67984

Other (OTH) AF: 0.0374 AC: 79 AN: 2112

Alfa AF: 0.0661 Hom.: 677

Bravo AF: 0.0430

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1950712; hg19: chr14-69480564;