4-187688564-C-T

Position:

• chr4-187688564-C-T

Variant summary

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

The ENST00000661504.1(ENSG00000249642):​n.370-16400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,896 control chromosomes in the GnomAD database, including 10,822 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 0.37 (10822 hom., cov: 33)
• Consequence: ENSG00000249642 ENST00000661504.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

Genes affected

ENSG00000249642 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983963	XR_939607.3	n.670+16110C>T		intron_variant
LOC107983963	XR_939608.2	n.605+14810C>T		intron_variant
LOC107983963	XR_939610.2	n.74+6165C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249642	ENST00000661504.1	n.370-16400C>T		intron_variant
ENSG00000249642	ENST00000663129.1	n.577-16400C>T		intron_variant
ENSG00000249642	ENST00000666084.1	n.407+16110C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56545 AN: 151778 Hom.: 10826 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.372 AC: 56558 AN: 151896 Hom.: 10822 Cov.: 33 AF XY: 0.371 AC XY: 27554 AN XY: 74206

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.368

Alfa AF: 0.357 Hom.: 1860

Bravo AF: 0.371

Asia WGS AF: 0.510 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996026; hg19: chr4-188609718;