chr5-165252619-C-T

Variant names:

• chr5-165252619-C-T
• rs10515894

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 0.0527 in 151,958 control chromosomes in the GnomAD database, including 299 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 0.053 (299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0984 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: 0.0527 AC: 7995 AN: 151840 Hom.: 298 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0398

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.0281

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0527 AC: 8010 AN: 151958 Hom.: 299 Cov.: 32 AF XY: 0.0523 AC XY: 3888 AN XY: 74280

African (AFR) AF: 0.101 AC: 4179 AN: 41408

American (AMR) AF: 0.0398 AC: 607 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3470

East Asian (EAS) AF: 0.0109 AC: 56 AN: 5150

South Asian (SAS) AF: 0.0666 AC: 320 AN: 4808

European-Finnish (FIN) AF: 0.0281 AC: 297 AN: 10578

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0320 AC: 2178 AN: 67968

Other (OTH) AF: 0.0577 AC: 122 AN: 2114

Alfa AF: 0.0469 Hom.: 37

Bravo AF: 0.0547

Asia WGS AF: 0.0520 AC: 183 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	8.1
DANN	Benign	0.84
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10515894; hg19: chr5-164679625;