rs6475535

Positions:

• chr9-21450475-G-C

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 0.241 in 152,130 control chromosomes in the GnomAD database, including 5,607 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 0.24 (5607 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21450475G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000698343.1	n.103-29783C>G		intron_variant
MIR31HG	ENST00000698344.1	n.496+26694C>G		intron_variant
MIR31HG	ENST00000698345.1	n.254+26694C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36507 AN: 152010 Hom.: 5576 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.241 AC: 36588 AN: 152130 Hom.: 5607 Cov.: 32 AF XY: 0.242 AC XY: 17970 AN XY: 74374

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.198

Alfa AF: 0.0974 Hom.: 139

Bravo AF: 0.246

Asia WGS AF: 0.279 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6475535; hg19: chr9-21450474;