rs7950811

Positions:

• chr11-92917836-C-A
• chr11-92917836-C-T

Variant summary

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

The ENST00000634657.1(ENSG00000290774):​n.81+1872C>A 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 0.0682 in 152,086 control chromosomes in the GnomAD database, including 419 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 0.068 (419 hom., cov: 33)
• Consequence: ENST00000634657.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 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
	ENST00000634657.1	n.81+1872C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 10345 AN: 151968 Hom.: 416 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0704

Gnomad SAS AF: 0.0415

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0682 AC: 10368 AN: 152086 Hom.: 419 Cov.: 33 AF XY: 0.0674 AC XY: 5012 AN XY: 74352

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0778

Gnomad4 ASJ AF: 0.0625

Gnomad4 EAS AF: 0.0709

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.0434

Gnomad4 NFE AF: 0.0424

Gnomad4 OTH AF: 0.0688

Alfa AF: 0.0450 Hom.: 426

Bravo AF: 0.0723

Asia WGS AF: 0.0760 AC: 264 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	0.75
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7950811; hg19: chr11-92651002;