rs11969002

Variant names:

• chr6-32891971-G-A
• rs11969002
• ENST00000753352.1:n.857-35C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32891971-G-A
• chr6-32891971-G-T

Variant summary

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

The ENST00000753352.1(ENSG00000289559):​n.857-35C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,150 control chromosomes in the GnomAD database, including 1,453 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 0.13 (1453 hom., cov: 32)
• Consequence: ENSG00000289559 ENST00000753352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 9 publications found

Genes affected

ENSG00000289559 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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
ENSG00000289559	ENST00000753352.1	n.857-35C>T		intron_variant	Intron 2 of 2
ENSG00000289559	ENST00000753353.1	n.508-35C>T		intron_variant	Intron 2 of 2
ENSG00000289559	ENST00000753354.1	n.416-35C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19603 AN: 152032 Hom.: 1447 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0952

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.129 AC: 19647 AN: 152150 Hom.: 1453 Cov.: 32 AF XY: 0.130 AC XY: 9642 AN XY: 74392

African (AFR) AF: 0.193 AC: 8023 AN: 41494

American (AMR) AF: 0.0952 AC: 1455 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.0867 AC: 450 AN: 5188

South Asian (SAS) AF: 0.142 AC: 684 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10580

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6835 AN: 67994

Other (OTH) AF: 0.121 AC: 255 AN: 2108

Alfa AF: 0.109 Hom.: 525

Bravo AF: 0.128

Asia WGS AF: 0.141 AC: 490 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	2.6
DANN	Benign	0.68
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11969002; hg19: chr6-32859748;