rs6911854

Variant names:

• chr6-78234822-T-C
• rs6911854
• ENST00000715178.1:n.1038-30869A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000715178.1(ENSG00000230309):​n.1038-30869A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000230309 ENST00000715178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 4 publications found

Genes affected

ENSG00000230309 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715178.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230309	ENST00000715178.1		n.1038-30869A>G		intron	N/A

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

African (AFR) AF: 0.375 AC: 15555 AN: 41458

American (AMR) AF: 0.298 AC: 4540 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3466

East Asian (EAS) AF: 0.488 AC: 2499 AN: 5126

South Asian (SAS) AF: 0.166 AC: 800 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1706 AN: 10568

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.130 AC: 8841 AN: 68000

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.214 Hom.: 784

Bravo AF: 0.255

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs6911854; hg19: chr6-78944539;