chr7-84698761-A-C

Variant names:

• chr7-84698761-A-C
• rs4329228
• ENST00000775795.1:n.73+21794T>G

Variant summary

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

The ENST00000775795.1(ENSG00000301054):​n.73+21794T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,792 control chromosomes in the GnomAD database, including 10,190 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 0.34 (10190 hom., cov: 32)
• Consequence: ENSG00000301054 ENST00000775795.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 2 publications found

Genes affected

ENSG00000301054 (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 = 0.535 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775795.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301054	ENST00000775795.1		n.73+21794T>G		intron	N/A
	ENSG00000301054	ENST00000775796.1		n.46+21794T>G		intron	N/A
	ENSG00000301054	ENST00000775800.1		n.96+21794T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50852 AN: 151674 Hom.: 10157 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.336 AC: 50934 AN: 151792 Hom.: 10190 Cov.: 32 AF XY: 0.332 AC XY: 24649 AN XY: 74188

African (AFR) AF: 0.541 AC: 22392 AN: 41372

American (AMR) AF: 0.362 AC: 5498 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2691 AN: 5148

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4824

European-Finnish (FIN) AF: 0.161 AC: 1695 AN: 10560

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15680 AN: 67918

Other (OTH) AF: 0.333 AC: 702 AN: 2106

Alfa AF: 0.258 Hom.: 2792

Bravo AF: 0.362

Asia WGS AF: 0.356 AC: 1225 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.46
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4329228; hg19: chr7-84328077;