4-99122133-C-T

Variant names:

• chr4-99122133-C-T
• rs2602891
• ENST00000500358.6:n.429-11422C>T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.429-11422C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,164 control chromosomes in the GnomAD database, including 48,099 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 0.79 (48099 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.429-11422C>T		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.429-11422C>T		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000661393.1	n.426-11422C>T		intron_variant	Intron 1 of 9
ENSG00000246090	ENST00000670724.1	n.481-11422C>T		intron_variant	Intron 1 of 2
ENSG00000246090	ENST00000691990.1	n.446+32849C>T		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.789 AC: 120026 AN: 152046 Hom.: 48045 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.790 AC: 120141 AN: 152164 Hom.: 48099 Cov.: 32 AF XY: 0.797 AC XY: 59279 AN XY: 74370

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.762

Alfa AF: 0.728 Hom.: 39101

Bravo AF: 0.796

Asia WGS AF: 0.932 AC: 3238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2602891; hg19: chr4-100043284;