rs7676384

Variant names:

• chr4-161252328-C-T
• rs7676384
• ENST00000816576.1:n.173-9247G>A

Variant summary

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

The ENST00000816576.1(ENSG00000306264):​n.173-9247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 150,234 control chromosomes in the GnomAD database, including 2,890 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 (2890 hom., cov: 31)
• Consequence: ENSG00000306264 ENST00000816576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 1 publications found

Genes affected

ENSG00000306264 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816576.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306264	ENST00000816576.1		n.173-9247G>A		intron	N/A
	ENSG00000306264	ENST00000816577.1		n.172-9247G>A		intron	N/A
	ENSG00000306264	ENST00000816580.1		n.186-7508G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 28968 AN: 150116 Hom.: 2883 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.193 AC: 29002 AN: 150234 Hom.: 2890 Cov.: 31 AF XY: 0.193 AC XY: 14183 AN XY: 73474

African (AFR) AF: 0.227 AC: 9057 AN: 39892

American (AMR) AF: 0.208 AC: 3164 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3468

East Asian (EAS) AF: 0.283 AC: 1453 AN: 5128

South Asian (SAS) AF: 0.141 AC: 679 AN: 4806

European-Finnish (FIN) AF: 0.139 AC: 1466 AN: 10514

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

European-Non Finnish (NFE) AF: 0.177 AC: 12021 AN: 67932

Other (OTH) AF: 0.191 AC: 399 AN: 2090

Alfa AF: 0.187 Hom.: 792

Bravo AF: 0.194

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.6
DANN	Benign	0.83
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7676384;

hg19: chr4-162173480;