1-209678552-A-G

Position:

• chr1-209678552-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.67-15491T>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 0.939 in 152,236 control chromosomes in the GnomAD database, including 67,422 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 0.94 (67422 hom., cov: 31)
• Consequence: HSD11B1-AS1 NR_134510.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSD11B1-AS1	NR_134510.1	n.67-15491T>C		intron_variant, non_coding_transcript_variant
HSD11B1-AS1	NR_134509.1	n.97-15491T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD11B1-AS1	ENST00000441672.1	n.97-15491T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142775 AN: 152118 Hom.: 67364 Cov.: 31

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.939 AC: 142892 AN: 152236 Hom.: 67422 Cov.: 31 AF XY: 0.935 AC XY: 69583 AN XY: 74424

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.945

Alfa AF: 0.941 Hom.: 96552

Bravo AF: 0.937

Asia WGS AF: 0.812 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4393158; hg19: chr1-209851897;