14-80120798-T-C

Variant names:

• chr14-80120798-T-C
• rs10220309

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 0.706 in 152,132 control chromosomes in the GnomAD database, including 38,311 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 0.71 (38311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107347 AN: 152016 Hom.: 38287 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.706 AC: 107412 AN: 152132 Hom.: 38311 Cov.: 32 AF XY: 0.705 AC XY: 52413 AN XY: 74366

African (AFR) AF: 0.739 AC: 30693 AN: 41516

American (AMR) AF: 0.585 AC: 8940 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2282 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3694 AN: 5146

South Asian (SAS) AF: 0.601 AC: 2896 AN: 4820

European-Finnish (FIN) AF: 0.776 AC: 8226 AN: 10596

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48393 AN: 67990

Other (OTH) AF: 0.694 AC: 1461 AN: 2106

Alfa AF: 0.705 Hom.: 18580

Bravo AF: 0.694

Asia WGS AF: 0.618 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.38
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10220309; hg19: chr14-80587141;