rs4545339

Positions:

• chr1-209739397-C-G
• chr1-209739397-C-T

Variant summary

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

The variant allele was found at a frequency of 0.052 in 152,144 control chromosomes in the GnomAD database, including 637 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 0.052 (637 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.209739397C>G		intergenic_region
HSD11B1-AS1	NR_134510.1	n.66+3100G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0521 AC: 7917 AN: 152026 Hom.: 634 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.0124

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0520 AC: 7916 AN: 152144 Hom.: 637 Cov.: 32 AF XY: 0.0574 AC XY: 4269 AN XY: 74388

Gnomad4 AFR AF: 0.0472

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.0985

Gnomad4 FIN AF: 0.0124

Gnomad4 NFE AF: 0.0123

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.00356 Hom.: 0

Bravo AF: 0.0648

Asia WGS AF: 0.160 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4545339; hg19: chr1-209912742;