14-83065771-C-T

Variant names:

• chr14-83065771-C-T
• rs8013489

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 0.664 in 151,840 control chromosomes in the GnomAD database, including 33,872 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 0.66 (33872 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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: 0.664 AC: 100717 AN: 151722 Hom.: 33839 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.664 AC: 100794 AN: 151840 Hom.: 33872 Cov.: 32 AF XY: 0.667 AC XY: 49537 AN XY: 74224

African (AFR) AF: 0.756 AC: 31345 AN: 41454

American (AMR) AF: 0.623 AC: 9482 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1844 AN: 3468

East Asian (EAS) AF: 0.811 AC: 4196 AN: 5174

South Asian (SAS) AF: 0.711 AC: 3427 AN: 4818

European-Finnish (FIN) AF: 0.617 AC: 6516 AN: 10560

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.617 AC: 41862 AN: 67844

Other (OTH) AF: 0.628 AC: 1323 AN: 2106

Alfa AF: 0.575 Hom.: 3087

Bravo AF: 0.665

Asia WGS AF: 0.720 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.61
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs8013489; hg19: chr14-83532115;