rs17780429

Variant names:

• chr6-137901451-G-A
• rs17780429
• ENST00000667736.2:n.731C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-137901451-G-A
• chr6-137901451-G-C
• chr6-137901451-G-T

Variant summary

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

The ENST00000667736.2(ENSG00000287393):​n.731C>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 0.11 in 152,034 control chromosomes in the GnomAD database, including 1,195 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 0.11 (1195 hom., cov: 31)
• Consequence: ENSG00000287393 ENST00000667736.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 12 publications found

Genes affected

ENSG00000287393 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.154 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
ENSG00000287393	ENST00000667736.2	n.731C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287393	ENST00000763344.1	n.304+429C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16789 AN: 151916 Hom.: 1195 Cov.: 31

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0365

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.110 AC: 16790 AN: 152034 Hom.: 1195 Cov.: 31 AF XY: 0.110 AC XY: 8170 AN XY: 74302

African (AFR) AF: 0.0275 AC: 1139 AN: 41490

American (AMR) AF: 0.159 AC: 2430 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.0366 AC: 189 AN: 5170

South Asian (SAS) AF: 0.107 AC: 514 AN: 4816

European-Finnish (FIN) AF: 0.136 AC: 1435 AN: 10562

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9950 AN: 67964

Other (OTH) AF: 0.116 AC: 245 AN: 2104

Alfa AF: 0.0877 Hom.: 166

Bravo AF: 0.110

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.39
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17780429; hg19: chr6-138222588;