rs9375225

Positions:

• chr6-98140878-G-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 0.415 in 151,878 control chromosomes in the GnomAD database, including 14,057 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 0.41 (14057 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.98140878G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000271860	ENST00000606913.5	n.240+41608G>T		intron_variant		5
ENSG00000271860	ENST00000607032.1	n.410+41608G>T		intron_variant		3
ENSG00000271860	ENST00000607823.5	n.352+41608G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62970 AN: 151762 Hom.: 14062 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.415 AC: 62966 AN: 151878 Hom.: 14057 Cov.: 32 AF XY: 0.411 AC XY: 30528 AN XY: 74200

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.417

Alfa AF: 0.454 Hom.: 1999

Bravo AF: 0.397

Asia WGS AF: 0.283 AC: 987 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.059
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9375225; hg19: chr6-98588754;