rs4958381

chr5-154651307-T-C

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 0.0648 in 152,112 control chromosomes in the GnomAD database, including 370 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 0.065 (370 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0648 AC: 9848 AN: 151994 Hom.: 368 Cov.: 31

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.0468

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0648 AC: 9864 AN: 152112 Hom.: 370 Cov.: 31 AF XY: 0.0665 AC XY: 4944 AN XY: 74374

Gnomad4 AFR AF: 0.0996

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.0468

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0390

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.0692

Alfa AF: 0.0533 Hom.: 26

Bravo AF: 0.0654

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.8
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4958381; hg19: chr5-154030867;