chr1-209671172-A-C

Position:

• chr1-209671172-A-C

Variant summary

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

The NR_134510.1(HSD11B1-AS1):​n.67-8111T>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 0.652 in 152,126 control chromosomes in the GnomAD database, including 33,789 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 0.65 (33789 hom., cov: 33)
• Consequence: HSD11B1-AS1 NR_134510.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD11B1-AS1	NR_134510.1	n.67-8111T>G		intron_variant, non_coding_transcript_variant
HSD11B1-AS1	NR_134509.1	n.97-8111T>G		intron_variant, non_coding_transcript_variant
HSD11B1-AS1	NR_134511.1	n.28+4050T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD11B1-AS1	ENST00000441672.1	n.97-8111T>G		intron_variant, non_coding_transcript_variant		3
HSD11B1-AS1	ENST00000445272.7	n.62+4050T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99137 AN: 152008 Hom.: 33774 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.652 AC: 99189 AN: 152126 Hom.: 33789 Cov.: 33 AF XY: 0.656 AC XY: 48794 AN XY: 74348

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.672

Alfa AF: 0.729 Hom.: 84172

Bravo AF: 0.640

Asia WGS AF: 0.631 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.5
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: rs4844486; hg19: chr1-209844517;