ENST00000685998.1:n.295+1211C>T

Variant names:

• chr6-27758952-C-T
• rs7776351
• ENST00000685998.1:n.295+1211C>T

Variant summary

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

The ENST00000685998.1(ENSG00000287252):​n.295+1211C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,098 control chromosomes in the GnomAD database, including 10,022 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 0.33 (10022 hom., cov: 32)
• Consequence: ENSG00000287252 ENST00000685998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

Genes affected

ENSG00000287252 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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
ENSG00000287252	ENST00000685998.1	n.295+1211C>T		intron_variant	Intron 1 of 4
ENSG00000287252	ENST00000689964.1	n.294+1214C>T		intron_variant	Intron 1 of 3
ENSG00000287252	ENST00000701586.1	n.325+1211C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50164 AN: 151980 Hom.: 9995 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.330 AC: 50235 AN: 152098 Hom.: 10022 Cov.: 32 AF XY: 0.324 AC XY: 24120 AN XY: 74344

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.308

Alfa AF: 0.251 Hom.: 10366

Bravo AF: 0.349

Asia WGS AF: 0.248 AC: 863 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7776351; hg19: chr6-27726731;