rs7112939

Positions:

• chr11-80322367-C-T

Variant summary

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

The ENST00000532605.1(ENSG00000254434):​n.79-241G>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 0.0472 in 151,874 control chromosomes in the GnomAD database, including 851 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 0.047 (851 hom., cov: 32)
• Consequence: ENST00000532605.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000532605.1	n.79-241G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7162 AN: 151756 Hom.: 849 Cov.: 32

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.0253

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.00465

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00359

Gnomad OTH AF: 0.0417

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

GnomAD4 genome AF: 0.0472 AC: 7170 AN: 151874 Hom.: 851 Cov.: 32 AF XY: 0.0534 AC XY: 3961 AN XY: 74192

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.0253

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.00465

Gnomad4 NFE AF: 0.00359

Gnomad4 OTH AF: 0.0427

Alfa AF: 0.0244 Hom.: 48

Bravo AF: 0.0647

Asia WGS AF: 0.197 AC: 683 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7112939; hg19: chr11-80033411;