rs11755943

Positions:

• chr6-26211140-A-G

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+86969A>G 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 0.167 in 152,224 control chromosomes in the GnomAD database, including 2,318 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 0.17 (2318 hom., cov: 32)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 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
	ENST00000707189.1	n.999+86969A>G		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1000+53019A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25478 AN: 152106 Hom.: 2321 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.167 AC: 25484 AN: 152224 Hom.: 2318 Cov.: 32 AF XY: 0.168 AC XY: 12486 AN XY: 74412

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.178

Alfa AF: 0.148 Hom.: 2308

Bravo AF: 0.169

Asia WGS AF: 0.156 AC: 545 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	1.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11755943; hg19: chr6-26211368;