rs1023849

Variant names:

• chr11-96856557-C-G
• rs1023849
• ENST00000661755.1:n.241+73319C>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 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: ENSG00000254587 ENST00000661755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

ENSG00000254587 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254587	ENST00000661755.1	n.241+73319C>G		intron_variant	Intron 3 of 4

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;