14-44660661-T-G

Variant names:

• chr14-44660661-T-G
• rs10484173

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.371 in 152,052 control chromosomes in the GnomAD database, including 11,307 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 (11307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 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: 0.371 AC: 56298 AN: 151934 Hom.: 11287 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.371 AC: 56358 AN: 152052 Hom.: 11307 Cov.: 32 AF XY: 0.365 AC XY: 27155 AN XY: 74340

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.392

Alfa AF: 0.325 Hom.: 16915

Bravo AF: 0.400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484173; hg19: chr14-45129864;