rs1016247

Variant names:

• chr14-96973814-A-G
• rs1016247

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 0.355 in 152,120 control chromosomes in the GnomAD database, including 10,017 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 0.35 (10017 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.463 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: 0.355 AC: 53987 AN: 152002 Hom.: 10023 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.355 AC: 53975 AN: 152120 Hom.: 10017 Cov.: 33 AF XY: 0.359 AC XY: 26729 AN XY: 74358

African (AFR) AF: 0.279 AC: 11590 AN: 41504

American (AMR) AF: 0.378 AC: 5772 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3470

East Asian (EAS) AF: 0.142 AC: 734 AN: 5186

South Asian (SAS) AF: 0.479 AC: 2311 AN: 4822

European-Finnish (FIN) AF: 0.424 AC: 4469 AN: 10550

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26644 AN: 67982

Other (OTH) AF: 0.340 AC: 718 AN: 2112

Alfa AF: 0.366 Hom.: 1506

Bravo AF: 0.347

Asia WGS AF: 0.290 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.36
DANN	Benign	0.54
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1016247; hg19: chr14-97440151;