rs4730430

Variant names:

• chr7-110407907-C-T
• rs4730430
• ENST00000658032.1:n.331-42617G>A

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.331-42617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,814 control chromosomes in the GnomAD database, including 13,718 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 0.42 (13718 hom., cov: 32)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 7 publications found

Genes affected

ENSG00000226965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375451	XR_927863.3	n.386+24904G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226965	ENST00000658032.1	n.331-42617G>A		intron_variant	Intron 3 of 5
ENSG00000226965	ENST00000666128.1	n.97+24904G>A		intron_variant	Intron 2 of 3
ENSG00000226965	ENST00000667232.1	n.411+24904G>A		intron_variant	Intron 4 of 7
ENSG00000226965	ENST00000843035.1	n.351+24904G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63752 AN: 151696 Hom.: 13712 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.420 AC: 63787 AN: 151814 Hom.: 13718 Cov.: 32 AF XY: 0.419 AC XY: 31105 AN XY: 74168

African (AFR) AF: 0.456 AC: 18857 AN: 41396

American (AMR) AF: 0.421 AC: 6403 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.175 AC: 904 AN: 5162

South Asian (SAS) AF: 0.240 AC: 1153 AN: 4814

European-Finnish (FIN) AF: 0.545 AC: 5747 AN: 10552

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.412 AC: 28005 AN: 67908

Other (OTH) AF: 0.412 AC: 869 AN: 2108

Alfa AF: 0.403 Hom.: 27645

Bravo AF: 0.414

Asia WGS AF: 0.212 AC: 742 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.5
DANN	Benign	0.84
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs4730430; hg19: chr7-110047964;