rs11968525

Variant names:

• chr6-159604175-G-A
• rs11968525
• ENST00000656085.1:n.42+58411C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656085.1(ENSG00000286533):​n.42+58411C>T variant causes a intron 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: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 5 publications found

Genes affected

ENSG00000286533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286533	ENST00000656085.1	n.42+58411C>T		intron_variant	Intron 1 of 1
ENSG00000286533	ENST00000794978.1	n.186-8971C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.413 AC: 17109 AN: 41384

American (AMR) AF: 0.181 AC: 2755 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3464

East Asian (EAS) AF: 0.180 AC: 930 AN: 5168

South Asian (SAS) AF: 0.228 AC: 1097 AN: 4810

European-Finnish (FIN) AF: 0.164 AC: 1732 AN: 10544

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11175 AN: 67960

Other (OTH) AF: 0.214 AC: 451 AN: 2106

Alfa AF: 0.215 Hom.: 747

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs11968525; hg19: chr6-160025207;