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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377515	XR_939409.1	n.-126G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306264	ENST00000816576.1	n.173-9247G>A		intron_variant	Intron 1 of 3
ENSG00000306264	ENST00000816577.1	n.172-9247G>A		intron_variant	Intron 1 of 2
ENSG00000306264	ENST00000816580.1	n.186-7508G>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs7676384; hg19: chr4-162173480;