ENST00000829574.1:n.435T>C

Variant names:

• chr6-10268831-T-C
• rs6940110
• ENST00000829574.1:n.435T>C

Variant summary

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

The ENST00000829574.1(ENSG00000307877):​n.435T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,098 control chromosomes in the GnomAD database, including 15,151 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 0.44 (15151 hom., cov: 33)
• Consequence: ENSG00000307877 ENST00000829574.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.822
• Publications: 6 publications found

Genes affected

ENSG00000307877 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829574.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307877	ENST00000829574.1		n.435T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307877	ENST00000829575.1		n.366T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000307859	ENST00000829457.1		n.525+64A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67023 AN: 151980 Hom.: 15136 Cov.: 33

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.441 AC: 67077 AN: 152098 Hom.: 15151 Cov.: 33 AF XY: 0.436 AC XY: 32426 AN XY: 74344

African (AFR) AF: 0.424 AC: 17600 AN: 41482

American (AMR) AF: 0.549 AC: 8391 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1739 AN: 3470

East Asian (EAS) AF: 0.147 AC: 760 AN: 5168

South Asian (SAS) AF: 0.475 AC: 2290 AN: 4818

European-Finnish (FIN) AF: 0.365 AC: 3853 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30589 AN: 67994

Other (OTH) AF: 0.485 AC: 1023 AN: 2108

Alfa AF: 0.454 Hom.: 66987

Bravo AF: 0.457

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.53
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs6940110; hg19: chr6-10269064;