rs6887695

chr5-159395637-G-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, non coding transcript 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: ENST00000635333.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000635333.1	n.327+3060G>C		intron_variant, non_coding_transcript_variant		5
	ENST00000641150.1	n.533-20887G>C		intron_variant, non_coding_transcript_variant
	ENST00000648969.1	n.54-20887G>C		intron_variant, non_coding_transcript_variant

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;