chr6-27758952-C-T

Position:

• chr6-27758952-C-T

Variant summary

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

The ENST00000702692.1(ENSG00000287252):​n.326+1211C>T variant causes a intron, non coding transcript 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: ENST00000702692.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702692.1	n.326+1211C>T		intron_variant, non_coding_transcript_variant

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;