rs911847

chr6-159647936-G-Achr6-159647936-G-T

Variant summary

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

The ENST00000656085.1(ENSG00000286533):n.42+14650C>T 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 0.31 in 151,948 control chromosomes in the GnomAD database, including 7,638 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 0.31 (7638 hom., cov: 31)
• Consequence: ENST00000656085.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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
	ENST00000656085.1	n.42+14650C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47062 AN: 151830 Hom.: 7626 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.310 AC: 47089 AN: 151948 Hom.: 7638 Cov.: 31 AF XY: 0.305 AC XY: 22657 AN XY: 74248

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.307

Alfa AF: 0.290 Hom.: 3434

Bravo AF: 0.319

Asia WGS AF: 0.254 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs911847; hg19: chr6-160068968;