rs4976691

Positions:

• chr5-177400814-C-G
• chr5-177400814-C-T

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 0.47 in 152,122 control chromosomes in the GnomAD database, including 21,016 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 0.47 (21016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 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: 0.470 AC: 71479 AN: 152004 Hom.: 21027 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.470 AC: 71455 AN: 152122 Hom.: 21016 Cov.: 32 AF XY: 0.469 AC XY: 34906 AN XY: 74372

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.522

Alfa AF: 0.532 Hom.: 3023

Bravo AF: 0.442

Asia WGS AF: 0.306 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4976691; hg19: chr5-176827815;