rs11940562

Positions:

• chr4-32591327-C-T

Variant summary

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

The ENST00000659320.1(ENSG00000286784):​n.216-6031G>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 0.183 in 151,790 control chromosomes in the GnomAD database, including 2,653 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 0.18 (2653 hom., cov: 32)
• Consequence: ENST00000659320.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 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
	ENST00000659320.1	n.216-6031G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27845 AN: 151672 Hom.: 2653 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.183 AC: 27850 AN: 151790 Hom.: 2653 Cov.: 32 AF XY: 0.183 AC XY: 13533 AN XY: 74130

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.193

Alfa AF: 0.194 Hom.: 1684

Bravo AF: 0.182

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11940562; hg19: chr4-32592949;