chr5-141042553-T-C

Variant names:

• chr5-141042553-T-C
• rs17119385

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.109 in 152,170 control chromosomes in the GnomAD database, including 1,118 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 0.11 (1118 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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: 0.109 AC: 16597 AN: 152054 Hom.: 1118 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0814

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.109 AC: 16620 AN: 152170 Hom.: 1118 Cov.: 32 AF XY: 0.108 AC XY: 8031 AN XY: 74418

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0814

Gnomad4 EAS AF: 0.0755

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.0771

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0467 Hom.: 49

Bravo AF: 0.111

Asia WGS AF: 0.0990 AC: 342 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	5.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17119385; hg19: chr5-140422138;