ENST00000769446.1:n.560+2140C>A

Variant names:

• chr1-87313534-G-T
• rs12118297
• ENST00000769446.1:n.560+2140C>A

Variant summary

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

The ENST00000769446.1(ENSG00000300145):​n.560+2140C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,184 control chromosomes in the GnomAD database, including 3,031 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 0.19 (3031 hom., cov: 33)
• Consequence: ENSG00000300145 ENST00000769446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 11 publications found

Genes affected

ENSG00000300145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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
ENSG00000300145	ENST00000769446.1	n.560+2140C>A		intron_variant	Intron 2 of 2
ENSG00000300145	ENST00000769447.1	n.522+2140C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29544 AN: 152066 Hom.: 3025 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.194 AC: 29561 AN: 152184 Hom.: 3031 Cov.: 33 AF XY: 0.200 AC XY: 14886 AN XY: 74380

African (AFR) AF: 0.194 AC: 8036 AN: 41512

American (AMR) AF: 0.164 AC: 2507 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1690 AN: 5176

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4820

European-Finnish (FIN) AF: 0.264 AC: 2790 AN: 10562

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12178 AN: 68022

Other (OTH) AF: 0.185 AC: 391 AN: 2116

Alfa AF: 0.179 Hom.: 495

Bravo AF: 0.186

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.46
DANN	Benign	0.41
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12118297; hg19: chr1-87779217;