rs72698613

Variant names:

• chr4-175087067-G-A
• rs72698613
• ENST00000658752.1:n.90-48344C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-175087067-G-A
• chr4-175087067-G-C

Variant summary

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

The ENST00000658752.1(ENSG00000248551):​n.90-48344C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0385 in 152,254 control chromosomes in the GnomAD database, including 151 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 0.038 (151 hom., cov: 32)
• Consequence: ENSG00000248551 ENST00000658752.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755
• Publications: 4 publications found

Genes affected

ENSG00000248551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0577 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
ENSG00000248551	ENST00000658752.1	n.90-48344C>T		intron_variant	Intron 1 of 1
ENSG00000248551	ENST00000798560.1	n.349-48344C>T		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.0385 AC: 5857 AN: 152136 Hom.: 151 Cov.: 32

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0607

Gnomad FIN AF: 0.0314

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0374

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

GnomAD4 genome AF: 0.0385 AC: 5860 AN: 152254 Hom.: 151 Cov.: 32 AF XY: 0.0371 AC XY: 2759 AN XY: 74454

African (AFR) AF: 0.0101 AC: 421 AN: 41556

American (AMR) AF: 0.0291 AC: 445 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0614 AC: 296 AN: 4822

European-Finnish (FIN) AF: 0.0314 AC: 333 AN: 10604

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4027 AN: 68016

Other (OTH) AF: 0.0370 AC: 78 AN: 2108

Alfa AF: 0.0525 Hom.: 310

Bravo AF: 0.0372

Asia WGS AF: 0.0190 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.76
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs72698613; hg19: chr4-176008218;