rs4075958

Positions:

• chr5-177357511-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.216 in 152,170 control chromosomes in the GnomAD database, including 4,125 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.22 (4125 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.315

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 5-177357511-G-A is Benign according to our data. Variant chr5-177357511-G-A is described in ClinVar as [Benign]. Clinvar id is 1235110.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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: 0.217 AC: 32933 AN: 152052 Hom.: 4123 Cov.: 33

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.216 AC: 32931 AN: 152170 Hom.: 4125 Cov.: 33 AF XY: 0.217 AC XY: 16177 AN XY: 74382

Gnomad4 AFR AF: 0.0988

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.214

Alfa AF: 0.261 Hom.: 11804

Bravo AF: 0.206

Asia WGS AF: 0.219 AC: 766 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 02, 2020

This variant is associated with the following publications: (PMID: 25526461) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075958; hg19: chr5-176784512;