rs7944342

Positions:

• chr11-32266398-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000525689.2(ENSG00000293378):​n.123-36037A>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 0.197 in 152,108 control chromosomes in the GnomAD database, including 3,443 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 0.20 (3443 hom., cov: 32)
• Consequence: ENST00000525689.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.51

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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
	ENST00000525689.2	n.123-36037A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29906 AN: 151990 Hom.: 3441 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.197 AC: 29909 AN: 152108 Hom.: 3443 Cov.: 32 AF XY: 0.196 AC XY: 14610 AN XY: 74390

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0213

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.213

Alfa AF: 0.230 Hom.: 2123

Bravo AF: 0.188

Asia WGS AF: 0.0720 AC: 249 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7944342; hg19: chr11-32287944;