rs10484009

Variant names:

• chr14-88908905-A-T
• rs10484009

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 0.0676 in 152,170 control chromosomes in the GnomAD database, including 820 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 0.068 (820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.0675 AC: 10268 AN: 152052 Hom.: 816 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0587

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00713

Gnomad OTH AF: 0.0537

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

GnomAD4 genome AF: 0.0676 AC: 10288 AN: 152170 Hom.: 820 Cov.: 32 AF XY: 0.0678 AC XY: 5042 AN XY: 74400

African (AFR) AF: 0.179 AC: 7416 AN: 41472

American (AMR) AF: 0.0589 AC: 901 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0253 AC: 88 AN: 3472

East Asian (EAS) AF: 0.160 AC: 825 AN: 5158

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4824

European-Finnish (FIN) AF: 0.0331 AC: 351 AN: 10608

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00713 AC: 485 AN: 68028

Other (OTH) AF: 0.0531 AC: 112 AN: 2108

Alfa AF: 0.0408 Hom.: 54

Bravo AF: 0.0752

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.68
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs10484009; hg19: chr14-89375249;