rs9468992

Positions:

• chr6-31416801-G-A

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 0.217 in 151,836 control chromosomes in the GnomAD database, including 4,278 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 0.22 (4278 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.46

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31416801G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.62+16038G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32849 AN: 151718 Hom.: 4270 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.217 AC: 32894 AN: 151836 Hom.: 4278 Cov.: 32 AF XY: 0.221 AC XY: 16445 AN XY: 74256

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.203

Alfa AF: 0.191 Hom.: 313

Bravo AF: 0.222

Asia WGS AF: 0.197 AC: 684 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.061
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9468992; hg19: chr6-31384578;