5-92963656-G-T

Variant names:

• chr5-92963656-G-T
• rs10514365

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 0.0167 in 152,148 control chromosomes in the GnomAD database, including 57 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 0.017 (57 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0506 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: 0.0167 AC: 2537 AN: 152032 Hom.: 57 Cov.: 32

Gnomad AFR AF: 0.00452

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0534

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.00425

Gnomad SAS AF: 0.00560

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0156

Gnomad OTH AF: 0.0226

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

GnomAD4 genome AF: 0.0167 AC: 2539 AN: 152148 Hom.: 57 Cov.: 32 AF XY: 0.0172 AC XY: 1278 AN XY: 74404

African (AFR) AF: 0.00450 AC: 187 AN: 41532

American (AMR) AF: 0.0536 AC: 818 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3466

East Asian (EAS) AF: 0.00426 AC: 22 AN: 5162

South Asian (SAS) AF: 0.00540 AC: 26 AN: 4814

European-Finnish (FIN) AF: 0.0249 AC: 264 AN: 10600

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0156 AC: 1059 AN: 68000

Other (OTH) AF: 0.0218 AC: 46 AN: 2106

Alfa AF: 0.00590 Hom.: 4

Bravo AF: 0.0196

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.64
DANN	Benign	0.71
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs10514365; hg19: chr5-92299363;