rs6912853

Variant names:

• chr6-26401210-C-T
• rs6912853
• ENST00000707189.1:n.1000-151977C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000707189.1(ENSG00000291336):​n.1000-151977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,140 control chromosomes in the GnomAD database, including 1,738 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 0.15 (1738 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291336	ENST00000707189.1	n.1000-151977C>T		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-131495C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22734 AN: 152022 Hom.: 1740 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.149 AC: 22734 AN: 152140 Hom.: 1738 Cov.: 32 AF XY: 0.151 AC XY: 11238 AN XY: 74358

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0791

Gnomad4 SAS AF: 0.0882

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.133

Alfa AF: 0.145 Hom.: 269

Bravo AF: 0.144

Asia WGS AF: 0.0780 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6912853; hg19: chr6-26401438;