5-151096443-T-C

Variant names:

• chr5-151096443-T-C
• rs1024995

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.189 in 152,098 control chromosomes in the GnomAD database, including 3,444 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 0.19 (3444 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 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: 0.189 AC: 28662 AN: 151980 Hom.: 3424 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.189 AC: 28721 AN: 152098 Hom.: 3444 Cov.: 32 AF XY: 0.192 AC XY: 14297 AN XY: 74352

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.199

Alfa AF: 0.129 Hom.: 1984

Bravo AF: 0.190

Asia WGS AF: 0.403 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024995; hg19: chr5-150476004;