rs6914539

Positions:

• chr6-103235862-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 0.0379 in 151,956 control chromosomes in the GnomAD database, including 334 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 0.038 (334 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.103235862C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5747 AN: 151840 Hom.: 332 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.000758

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00346

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0379 AC: 5766 AN: 151956 Hom.: 334 Cov.: 32 AF XY: 0.0373 AC XY: 2774 AN XY: 74286

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0180

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.00194

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.000758

Gnomad4 NFE AF: 0.00346

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0306 Hom.: 19

Bravo AF: 0.0437

Asia WGS AF: 0.0270 AC: 92 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6914539; hg19: chr6-103683737;