rs4075958

Variant names:

• chr5-177357511-G-A
• rs4075958

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 63 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0988 AC: 4104 AN: 41544

American (AMR) AF: 0.237 AC: 3627 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3472

East Asian (EAS) AF: 0.152 AC: 788 AN: 5172

South Asian (SAS) AF: 0.265 AC: 1275 AN: 4820

European-Finnish (FIN) AF: 0.291 AC: 3082 AN: 10590

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18440 AN: 67970

Other (OTH) AF: 0.214 AC: 452 AN: 2108

Alfa AF: 0.250 Hom.: 18306

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

Nov 02, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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
PhyloP100		0.32
PromoterAI		0.026	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4075958; hg19: chr5-176784512;