rs4958381

Variant names:

• chr5-154651307-T-C
• rs4958381

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 0.0648 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0996 AC: 4133 AN: 41492

American (AMR) AF: 0.0648 AC: 990 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0468 AC: 162 AN: 3464

East Asian (EAS) AF: 0.116 AC: 599 AN: 5172

South Asian (SAS) AF: 0.123 AC: 590 AN: 4814

European-Finnish (FIN) AF: 0.0390 AC: 412 AN: 10576

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0413 AC: 2809 AN: 67992

Other (OTH) AF: 0.0692 AC: 146 AN: 2110

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4958381; hg19: chr5-154030867;