ENST00000500358.6:n.4161-1216G>T

Variant names:

• chr4-99299083-G-T
• rs13103321
• ENST00000500358.6:n.4161-1216G>T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.4161-1216G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,032 control chromosomes in the GnomAD database, including 6,979 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 0.27 (6979 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 9 publications found

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.4161-1216G>T		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.4161-1216G>T		intron_variant	Intron 7 of 9	1
ENSG00000246090	ENST00000509939.1	n.71-1216G>T		intron_variant	Intron 1 of 3	3
ENSG00000246090	ENST00000661393.1	n.1269-1216G>T		intron_variant	Intron 7 of 9

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41471 AN: 151914 Hom.: 6984 Cov.: 32

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.273 AC: 41471 AN: 152032 Hom.: 6979 Cov.: 32 AF XY: 0.267 AC XY: 19839 AN XY: 74328

African (AFR) AF: 0.0997 AC: 4134 AN: 41470

American (AMR) AF: 0.261 AC: 3976 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3468

East Asian (EAS) AF: 0.0262 AC: 136 AN: 5182

South Asian (SAS) AF: 0.150 AC: 722 AN: 4818

European-Finnish (FIN) AF: 0.358 AC: 3783 AN: 10560

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25955 AN: 67962

Other (OTH) AF: 0.316 AC: 666 AN: 2106

Alfa AF: 0.356 Hom.: 15500

Bravo AF: 0.258

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.24
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs13103321; hg19: chr4-100220240;