chr4-23628426-A-G

Variant names:

• chr4-23628426-A-G
• rs16873946
• ENST00000514290.1:n.117+67387A>G

Variant summary

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

The ENST00000514290.1(ENSG00000250137):​n.117+67387A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00525 in 152,178 control chromosomes in the GnomAD database, including 22 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 0.0053 (22 hom., cov: 32)
• Consequence: ENSG00000250137 ENST00000514290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265

Genes affected

ENSG00000250137 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250137	ENST00000514290.1	n.117+67387A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.00526 AC: 800 AN: 152060 Hom.: 22 Cov.: 32

Gnomad AFR AF: 0.00282

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000657

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0662

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.00334

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

GnomAD4 genome AF: 0.00525 AC: 799 AN: 152178 Hom.: 22 Cov.: 32 AF XY: 0.00641 AC XY: 477 AN XY: 74394

Gnomad4 AFR AF: 0.00284

Gnomad4 AMR AF: 0.000656

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0663

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000103

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00132 Hom.: 1

Bravo AF: 0.00366

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16873946; hg19: chr4-23630049;