rs10514465

Positions:

• chr16-79646955-G-T

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 0.431 in 152,064 control chromosomes in the GnomAD database, including 15,003 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 0.43 (15003 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65524 AN: 151946 Hom.: 14997 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.431 AC: 65549 AN: 152064 Hom.: 15003 Cov.: 33 AF XY: 0.430 AC XY: 31982 AN XY: 74358

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.434

Alfa AF: 0.463 Hom.: 2151

Bravo AF: 0.407

Asia WGS AF: 0.347 AC: 1208 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	0.19
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514465; hg19: chr16-79680852;