chr5-141042553-T-C

Position:

• chr5-141042553-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;