chr7-132023522-T-C

Variant names:

• chr7-132023522-T-C
• rs7811818
• ENST00000774478.1:n.73A>G

Variant summary

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

The ENST00000774478.1(ENSG00000300842):​n.73A>G 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 0.867 in 152,218 control chromosomes in the GnomAD database, including 57,371 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 0.87 (57371 hom., cov: 32)
• Consequence: ENSG00000300842 ENST00000774478.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 2 publications found

Genes affected

ENSG00000300842 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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
ENSG00000300842	ENST00000774478.1	n.73A>G		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131788 AN: 152100 Hom.: 57311 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.867 AC: 131911 AN: 152218 Hom.: 57371 Cov.: 32 AF XY: 0.868 AC XY: 64584 AN XY: 74424

African (AFR) AF: 0.917 AC: 38094 AN: 41544

American (AMR) AF: 0.879 AC: 13445 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2782 AN: 3468

East Asian (EAS) AF: 0.985 AC: 5095 AN: 5172

South Asian (SAS) AF: 0.908 AC: 4388 AN: 4832

European-Finnish (FIN) AF: 0.847 AC: 8973 AN: 10592

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56414 AN: 68012

Other (OTH) AF: 0.852 AC: 1795 AN: 2108

Alfa AF: 0.842 Hom.: 24803

Bravo AF: 0.871

Asia WGS AF: 0.930 AC: 3234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs7811818; hg19: chr7-131708281;