rs11968525

chr6-159604175-G-A

Variant summary

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

The ENST00000656085.1(ENSG00000286533):n.42+58411C>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 0.237 in 151,900 control chromosomes in the GnomAD database, including 5,185 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 0.24 (5185 hom., cov: 31)
• Consequence: ENST00000656085.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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+58411C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36035 AN: 151782 Hom.: 5180 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.0441

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.237 AC: 36067 AN: 151900 Hom.: 5185 Cov.: 31 AF XY: 0.236 AC XY: 17522 AN XY: 74242

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.214

Alfa AF: 0.208 Hom.: 669

Bravo AF: 0.245

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11968525; hg19: chr6-160025207;