rs6911854

Positions:

• chr6-78234822-T-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 0.232 in 152,000 control chromosomes in the GnomAD database, including 5,305 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 0.23 (5305 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78234822T>C		intergenic_region
LOC105377865	XR_002956359.2	n.135-30869A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35281 AN: 151880 Hom.: 5300 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.232 AC: 35312 AN: 152000 Hom.: 5305 Cov.: 32 AF XY: 0.235 AC XY: 17475 AN XY: 74290

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.218

Alfa AF: 0.209 Hom.: 727

Bravo AF: 0.255

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6911854; hg19: chr6-78944539;