5-68347127-C-T

Variant names:

• chr5-68347127-C-T
• rs10515079

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 0.176 in 152,072 control chromosomes in the GnomAD database, including 2,553 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 0.18 (2553 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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: 0.176 AC: 26811 AN: 151954 Hom.: 2555 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.176 AC: 26825 AN: 152072 Hom.: 2553 Cov.: 33 AF XY: 0.174 AC XY: 12899 AN XY: 74340

African (AFR) AF: 0.223 AC: 9245 AN: 41436

American (AMR) AF: 0.127 AC: 1936 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3468

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5188

South Asian (SAS) AF: 0.0567 AC: 273 AN: 4818

European-Finnish (FIN) AF: 0.210 AC: 2219 AN: 10582

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12235 AN: 67978

Other (OTH) AF: 0.154 AC: 325 AN: 2108

Alfa AF: 0.127 Hom.: 244

Bravo AF: 0.171

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.24
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10515079; hg19: chr5-67642955;