chr7-30906312-A-C

Variant names:

• chr7-30906312-A-C
• rs7788618
• ENST00000509504.2:c.621-5681A>C

Variant summary

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

The ENST00000509504.2(ENSG00000250424):​c.621-5681A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,120 control chromosomes in the GnomAD database, including 9,569 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 0.30 (9569 hom., cov: 33)
• Consequence: ENSG00000250424 ENST00000509504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887
• Publications: 1 publications found

Genes affected

ENSG00000250424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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
ENSG00000250424	ENST00000509504.2	c.621-5681A>C		intron_variant	Intron 7 of 10	5		ENSP00000421315.2

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45237 AN: 152002 Hom.: 9523 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.298 AC: 45344 AN: 152120 Hom.: 9569 Cov.: 33 AF XY: 0.298 AC XY: 22151 AN XY: 74374

African (AFR) AF: 0.605 AC: 25100 AN: 41504

American (AMR) AF: 0.233 AC: 3558 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3466

East Asian (EAS) AF: 0.170 AC: 878 AN: 5156

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4816

European-Finnish (FIN) AF: 0.158 AC: 1673 AN: 10598

Middle Eastern (MID) AF: 0.262 AC: 76 AN: 290

European-Non Finnish (NFE) AF: 0.166 AC: 11290 AN: 67974

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.184 Hom.: 1660

Bravo AF: 0.314

Asia WGS AF: 0.315 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		0.89
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7788618; hg19: chr7-30945927;