rs4730721

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000243243 (HGNC:):

ENSG00000237813 (HGNC:40129):

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 (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

African (AFR) AF: 0.525 AC: 21699 AN: 41360

American (AMR) AF: 0.428 AC: 6523 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2936 AN: 5136

South Asian (SAS) AF: 0.411 AC: 1976 AN: 4802

European-Finnish (FIN) AF: 0.424 AC: 4442 AN: 10488

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26926 AN: 67886

Other (OTH) AF: 0.429 AC: 903 AN: 2106

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
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs4730721; hg19: chr7-115899335;