chr14-85070100-C-T

Variant names:

• chr14-85070100-C-T
• rs10220453

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 0.268 in 151,714 control chromosomes in the GnomAD database, including 6,498 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 0.27 (6498 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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: 0.268 AC: 40636 AN: 151598 Hom.: 6477 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.268 AC: 40700 AN: 151714 Hom.: 6498 Cov.: 31 AF XY: 0.266 AC XY: 19736 AN XY: 74094

African (AFR) AF: 0.450 AC: 18621 AN: 41384

American (AMR) AF: 0.166 AC: 2528 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3462

East Asian (EAS) AF: 0.182 AC: 934 AN: 5126

South Asian (SAS) AF: 0.232 AC: 1117 AN: 4806

European-Finnish (FIN) AF: 0.223 AC: 2350 AN: 10540

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13787 AN: 67862

Other (OTH) AF: 0.226 AC: 476 AN: 2102

Alfa AF: 0.216 Hom.: 3399

Bravo AF: 0.272

Asia WGS AF: 0.218 AC: 758 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.39
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10220453; hg19: chr14-85536444;