rs6894758

Variant names:

• chr5-71718885-T-C
• rs6894758

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 0.175 in 152,132 control chromosomes in the GnomAD database, including 3,234 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (3234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.311
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 5-71718885-T-C is Benign according to our data. Variant chr5-71718885-T-C is described in ClinVar as Benign. ClinVar VariationId is 1175702.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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: 0.175 AC: 26624 AN: 152014 Hom.: 3228 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.175 AC: 26665 AN: 152132 Hom.: 3234 Cov.: 32 AF XY: 0.170 AC XY: 12667 AN XY: 74378

African (AFR) AF: 0.344 AC: 14251 AN: 41462

American (AMR) AF: 0.118 AC: 1799 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 508 AN: 3468

East Asian (EAS) AF: 0.121 AC: 624 AN: 5170

South Asian (SAS) AF: 0.147 AC: 708 AN: 4814

European-Finnish (FIN) AF: 0.0669 AC: 710 AN: 10606

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7426 AN: 68000

Other (OTH) AF: 0.174 AC: 367 AN: 2110

Alfa AF: 0.129 Hom.: 796

Bravo AF: 0.187

Asia WGS AF: 0.133 AC: 465 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.38
PhyloP100		-0.31
PromoterAI		0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6894758; hg19: chr5-71014712; COSMIC: COSV57115881;