rs846908

chr1-209685108-A-G

Variant summary

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

The NR_134510.1(HSD11B1-AS1):n.67-22047T>C 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 0.961 in 152,356 control chromosomes in the GnomAD database, including 70,695 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 0.96 (70695 hom., cov: 32)
• Consequence: HSD11B1-AS1 NR_134510.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517

Genes affected

HSD11B1-AS1 (HGNC:54053): (HSD11B1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD11B1-AS1	NR_134510.1	n.67-22047T>C		intron_variant, non_coding_transcript_variant
HSD11B1-AS1	NR_134509.1	n.97-22047T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD11B1-AS1	ENST00000441672.1	n.97-22047T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146361 AN: 152238 Hom.: 70636 Cov.: 32

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.961 AC: 146478 AN: 152356 Hom.: 70695 Cov.: 32 AF XY: 0.958 AC XY: 71362 AN XY: 74494

Gnomad4 AFR AF: 0.993

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.987

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.966

Alfa AF: 0.967 Hom.: 116480

Bravo AF: 0.957

Asia WGS AF: 0.844 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.35
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs846908; hg19: chr1-209858453;