chr4-99118696-T-A

Variant names:

• chr4-99118696-T-A
• rs2602877
• ENST00000500358.6:n.429-14859T>A

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.429-14859T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,132 control chromosomes in the GnomAD database, including 48,464 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 (48464 hom., cov: 31)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 6 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=-0.87).
• 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.429-14859T>A		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.429-14859T>A		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000661393.1	n.426-14859T>A		intron_variant	Intron 1 of 9
ENSG00000246090	ENST00000670724.2	n.481-14859T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120533 AN: 152014 Hom.: 48410 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.793 AC: 120647 AN: 152132 Hom.: 48464 Cov.: 31 AF XY: 0.800 AC XY: 59522 AN XY: 74374

African (AFR) AF: 0.891 AC: 36981 AN: 41500

American (AMR) AF: 0.799 AC: 12216 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5171 AN: 5180

South Asian (SAS) AF: 0.884 AC: 4256 AN: 4816

European-Finnish (FIN) AF: 0.774 AC: 8182 AN: 10576

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.720 AC: 48962 AN: 67992

Other (OTH) AF: 0.765 AC: 1618 AN: 2114

Alfa AF: 0.758 Hom.: 5491

Bravo AF: 0.800

Asia WGS AF: 0.932 AC: 3237 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.84
DANN	Benign	0.79
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2602877; hg19: chr4-100039847;