rs11753837

Variant names:

• chr6-26190519-G-A
• rs11753837
• ENST00000707189.1:n.999+66348G>A

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+66348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,126 control chromosomes in the GnomAD database, including 911 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 0.11 (911 hom., cov: 31)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 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
ENSG00000291336	ENST00000707189.1	n.999+66348G>A		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1000+32398G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16118 AN: 152008 Hom.: 914 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0970

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.106 AC: 16126 AN: 152126 Hom.: 911 Cov.: 31 AF XY: 0.107 AC XY: 7940 AN XY: 74384

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0971

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0995 Hom.: 1020

Bravo AF: 0.103

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.71
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11753837; hg19: chr6-26190747;