14-65810939-G-A

Variant names:

• chr14-65810939-G-A
• rs10149555

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 0.366 in 152,056 control chromosomes in the GnomAD database, including 11,289 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 0.37 (11289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55576 AN: 151936 Hom.: 11288 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.366 AC: 55605 AN: 152056 Hom.: 11289 Cov.: 33 AF XY: 0.373 AC XY: 27747 AN XY: 74338

African (AFR) AF: 0.192 AC: 7941 AN: 41462

American (AMR) AF: 0.335 AC: 5124 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3470

East Asian (EAS) AF: 0.471 AC: 2436 AN: 5170

South Asian (SAS) AF: 0.515 AC: 2479 AN: 4818

European-Finnish (FIN) AF: 0.520 AC: 5493 AN: 10566

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29681 AN: 67986

Other (OTH) AF: 0.374 AC: 786 AN: 2104

Alfa AF: 0.403 Hom.: 37819

Bravo AF: 0.342

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.20
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs10149555; hg19: chr14-66277657;