rs6887695

Variant names:

• chr5-159395637-G-C
• rs6887695
• ENST00000635333.1:n.327+3060G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635333.1(ENSG00000249738):​n.327+3060G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,962 control chromosomes in the GnomAD database, including 9,329 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 0.35 (9329 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 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
ENSG00000249738	ENST00000635333.1	n.327+3060G>C		intron_variant	Intron 4 of 7	5
ENSG00000249738	ENST00000641150.1	n.533-20887G>C		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.54-20887G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52573 AN: 151844 Hom.: 9315 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.346 AC: 52621 AN: 151962 Hom.: 9329 Cov.: 32 AF XY: 0.346 AC XY: 25693 AN XY: 74262

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.359

Alfa AF: 0.322 Hom.: 4297

Bravo AF: 0.353

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6887695; hg19: chr5-158822645;