rs944664

Positions:

• chr6-85179257-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 0.346 in 152,010 control chromosomes in the GnomAD database, including 9,970 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 0.35 (9970 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85179257C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52552 AN: 151892 Hom.: 9970 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.346 AC: 52581 AN: 152010 Hom.: 9970 Cov.: 33 AF XY: 0.352 AC XY: 26130 AN XY: 74294

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.352

Alfa AF: 0.281 Hom.: 2788

Bravo AF: 0.366

Asia WGS AF: 0.509 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs944664; hg19: chr6-85888975;