rs1023849

chr11-96856557-C-G

Variant summary

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

The ENST00000661755.1(ENSG00000254587):n.241+73319C>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 0.301 in 151,654 control chromosomes in the GnomAD database, including 8,024 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 0.30 (8024 hom., cov: 32)
• Consequence: ENST00000661755.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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
	ENST00000661755.1	n.241+73319C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45621 AN: 151534 Hom.: 8022 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.301 AC: 45634 AN: 151654 Hom.: 8024 Cov.: 32 AF XY: 0.300 AC XY: 22259 AN XY: 74114

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.260

Alfa AF: 0.342 Hom.: 1214

Bravo AF: 0.282

Asia WGS AF: 0.213 AC: 743 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.45
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023849; hg19: chr11-96727557;