rs10892258

Positions:

• chr11-118709156-G-A

Variant summary

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

The ENST00000526274.2(ENSG00000255422):​n.373+633G>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 0.195 in 152,074 control chromosomes in the GnomAD database, including 3,229 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 (3229 hom., cov: 32)
• Consequence: ENST00000526274.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369519	XR_948070.3	n.799G>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000526274.2	n.373+633G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000646572.2	n.1235G>A		non_coding_transcript_exon_variant	3/3
	ENST00000702882.1	n.1164G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29709 AN: 151956 Hom.: 3226 Cov.: 32

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.195 AC: 29712 AN: 152074 Hom.: 3229 Cov.: 32 AF XY: 0.198 AC XY: 14727 AN XY: 74334

Gnomad4 AFR AF: 0.0984

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.190

Alfa AF: 0.225 Hom.: 2049

Bravo AF: 0.184

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10892258; hg19: chr11-118579865;