ENST00000780084.1:n.192+42724T>C

Variant names:

• chr6-121810339-T-C
• rs1015451
• ENST00000780084.1:n.192+42724T>C

Variant summary

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

The ENST00000780084.1(ENSG00000289871):​n.192+42724T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,032 control chromosomes in the GnomAD database, including 6,510 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 0.23 (6510 hom., cov: 32)
• Consequence: ENSG00000289871 ENST00000780084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 20 publications found

Genes affected

ENSG00000289871 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377979	XR_942936.3	n.237+42724T>C		intron_variant	Intron 1 of 6
LOC105377979	XR_942937.4	n.237+42724T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289871	ENST00000780084.1	n.192+42724T>C		intron_variant	Intron 1 of 4
ENSG00000289871	ENST00000780085.1	n.79+42724T>C		intron_variant	Intron 1 of 3
ENSG00000289871	ENST00000780086.1	n.108+42724T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34522 AN: 151914 Hom.: 6477 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0981

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.228 AC: 34602 AN: 152032 Hom.: 6510 Cov.: 32 AF XY: 0.226 AC XY: 16828 AN XY: 74322

African (AFR) AF: 0.505 AC: 20908 AN: 41442

American (AMR) AF: 0.121 AC: 1854 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0981 AC: 340 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2321 AN: 5152

South Asian (SAS) AF: 0.108 AC: 520 AN: 4822

European-Finnish (FIN) AF: 0.131 AC: 1390 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0997 AC: 6779 AN: 67978

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.171 Hom.: 5641

Bravo AF: 0.241

Asia WGS AF: 0.301 AC: 1043 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.77
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1015451; hg19: chr6-122131485;