rs7530323

Variant names:

• chr1-38435020-G-A
• rs7530323
• ENST00000779046.1:n.260+7398G>A

Variant summary

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

The ENST00000779046.1(ENSG00000301471):​n.260+7398G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,106 control chromosomes in the GnomAD database, including 9,804 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 0.35 (9804 hom., cov: 32)
• Consequence: ENSG00000301471 ENST00000779046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815
• Publications: 3 publications found

Genes affected

ENSG00000301471 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779046.1. 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
	ENSG00000301471	ENST00000779046.1		n.260+7398G>A		intron	N/A
	ENSG00000301471	ENST00000779047.1		n.260+7398G>A		intron	N/A
	ENSG00000301471	ENST00000779048.1		n.260+7398G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53272 AN: 151988 Hom.: 9804 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.350 AC: 53287 AN: 152106 Hom.: 9804 Cov.: 32 AF XY: 0.349 AC XY: 25978 AN XY: 74348

African (AFR) AF: 0.282 AC: 11721 AN: 41494

American (AMR) AF: 0.305 AC: 4653 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3468

East Asian (EAS) AF: 0.121 AC: 623 AN: 5170

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4818

European-Finnish (FIN) AF: 0.414 AC: 4373 AN: 10572

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27553 AN: 67994

Other (OTH) AF: 0.368 AC: 777 AN: 2110

Alfa AF: 0.366 Hom.: 1831

Bravo AF: 0.337

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.62
PhyloP100		0.81

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: rs7530323;

hg19: chr1-38900692;