7-12020180-T-G

Variant names:

• chr7-12020180-T-G
• rs769111
• ENST00000775347.1:n.290+74473A>C

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.290+74473A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,796 control chromosomes in the GnomAD database, including 13,953 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 0.42 (13953 hom., cov: 31)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 8 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901589	XR_007060211.1	n.85+74473A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300984	ENST00000775347.1	n.290+74473A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63731 AN: 151678 Hom.: 13918 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.420 AC: 63815 AN: 151796 Hom.: 13953 Cov.: 31 AF XY: 0.418 AC XY: 30962 AN XY: 74158

African (AFR) AF: 0.544 AC: 22509 AN: 41376

American (AMR) AF: 0.387 AC: 5899 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1772 AN: 3460

East Asian (EAS) AF: 0.294 AC: 1514 AN: 5150

South Asian (SAS) AF: 0.384 AC: 1846 AN: 4812

European-Finnish (FIN) AF: 0.376 AC: 3958 AN: 10534

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25158 AN: 67902

Other (OTH) AF: 0.408 AC: 861 AN: 2108

Alfa AF: 0.401 Hom.: 13161

Bravo AF: 0.427

Asia WGS AF: 0.353 AC: 1227 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	0.41
DANN	Benign	0.71
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs769111; hg19: chr7-12059806;