rs4730721

Variant names:

• chr7-116259281-T-A
• rs4730721
• ENST00000444244.1:n.66-4046A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444244.1(ENSG00000243243):​n.66-4046A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,696 control chromosomes in the GnomAD database, including 15,148 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 0.44 (15148 hom., cov: 30)
• Consequence: ENSG00000243243 ENST00000444244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

Genes affected

ENSG00000243243 (HGNC:):

ENSG00000237813 (HGNC:40129):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 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
ENSG00000243243	ENST00000444244.1	n.66-4046A>T		intron_variant	Intron 1 of 4	3
ENSG00000237813	ENST00000446355.2	n.204-15345A>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67328 AN: 151586 Hom.: 15134 Cov.: 30

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.444 AC: 67390 AN: 151696 Hom.: 15148 Cov.: 30 AF XY: 0.448 AC XY: 33204 AN XY: 74130

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.429

Alfa AF: 0.429 Hom.: 1785

Bravo AF: 0.450

Asia WGS AF: 0.538 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4730721; hg19: chr7-115899335;