rs2602846

Variant names:

• chr4-99104000-T-A
• rs2602846
• ENST00000500358.6:n.428+14716T>A

Your query was ambiguous. Multiple possible variants found:

• chr4-99104000-T-A
• chr4-99104000-T-G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.428+14716T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,100 control chromosomes in the GnomAD database, including 47,889 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 (47889 hom., cov: 31)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 2 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=-0.97).
• 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.428+14716T>A		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.428+14716T>A		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000661393.1	n.425+14716T>A		intron_variant	Intron 1 of 9
ENSG00000246090	ENST00000670724.2	n.480+14716T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119859 AN: 151982 Hom.: 47837 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.789 AC: 119972 AN: 152100 Hom.: 47889 Cov.: 31 AF XY: 0.797 AC XY: 59225 AN XY: 74352

African (AFR) AF: 0.876 AC: 36364 AN: 41528

American (AMR) AF: 0.798 AC: 12192 AN: 15278

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: 4269 AN: 4828

European-Finnish (FIN) AF: 0.774 AC: 8169 AN: 10552

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

European-Non Finnish (NFE) AF: 0.720 AC: 48936 AN: 67948

Other (OTH) AF: 0.761 AC: 1610 AN: 2116

Alfa AF: 0.755 Hom.: 5453

Bravo AF: 0.794

Asia WGS AF: 0.931 AC: 3236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.75
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs2602846; hg19: chr4-100025151;