4-99202029-A-G

Variant names:

• chr4-99202029-A-G
• rs2051428
• ENST00000500358.6:n.3715-2328A>G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3715-2328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,030 control chromosomes in the GnomAD database, including 6,152 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 0.26 (6152 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500358.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100507053	NR_037884.1		n.3715-2328A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246090	ENST00000500358.6	TSL:1	n.3715-2328A>G		intron	N/A
	ENSG00000246090	ENST00000506160.1	TSL:4	n.333-2328A>G		intron	N/A
	ENSG00000246090	ENST00000506454.2	TSL:3	n.98-2328A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40205 AN: 151912 Hom.: 6155 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.264 AC: 40203 AN: 152030 Hom.: 6152 Cov.: 32 AF XY: 0.265 AC XY: 19697 AN XY: 74334

African (AFR) AF: 0.278 AC: 11528 AN: 41416

American (AMR) AF: 0.198 AC: 3028 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3468

East Asian (EAS) AF: 0.773 AC: 3994 AN: 5168

South Asian (SAS) AF: 0.420 AC: 2020 AN: 4814

European-Finnish (FIN) AF: 0.151 AC: 1605 AN: 10602

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16273 AN: 67974

Other (OTH) AF: 0.260 AC: 550 AN: 2116

Alfa AF: 0.250 Hom.: 8608

Bravo AF: 0.266

Asia WGS AF: 0.441 AC: 1531 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2051428;

hg19: chr4-100123186;

COSMIC: COSV52954825;