chr6-170139836-C-T

Variant names:

• chr6-170139836-C-T
• rs4710758
• ENST00000801741.1:n.2119C>T

Variant summary

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

The ENST00000801741.1(ENSG00000288162):​n.2119C>T 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 0.251 in 152,162 control chromosomes in the GnomAD database, including 5,466 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 0.25 (5466 hom., cov: 34)
• Consequence: ENSG00000288162 ENST00000801741.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 9 publications found

Genes affected

ENSG00000288162 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 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
ENSG00000288162	ENST00000801741.1	n.2119C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000288162	ENST00000671798.1	n.99-688C>T		intron_variant	Intron 1 of 2
ENSG00000289623	ENST00000801401.1	n.114-688C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38103 AN: 152046 Hom.: 5451 Cov.: 34

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.251 AC: 38153 AN: 152162 Hom.: 5466 Cov.: 34 AF XY: 0.253 AC XY: 18786 AN XY: 74378

African (AFR) AF: 0.118 AC: 4882 AN: 41546

American (AMR) AF: 0.321 AC: 4902 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 991 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1451 AN: 5158

South Asian (SAS) AF: 0.231 AC: 1115 AN: 4828

European-Finnish (FIN) AF: 0.356 AC: 3763 AN: 10582

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20402 AN: 67968

Other (OTH) AF: 0.249 AC: 527 AN: 2114

Alfa AF: 0.275 Hom.: 16118

Bravo AF: 0.242

Asia WGS AF: 0.283 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.57
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4710758; hg19: chr6-170455060;