4-187000345-A-T

Position:

• chr4-187000345-A-T

Variant summary

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

The ENST00000503037.2(ENSG00000249742):​n.245-3907T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,044 control chromosomes in the GnomAD database, including 15,447 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 0.42 (15447 hom., cov: 33)
• Consequence: ENST00000503037.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723906	XR_007058501.1	n.329-19476A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000503037.2	n.245-3907T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63083 AN: 151926 Hom.: 15410 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.415 AC: 63173 AN: 152044 Hom.: 15447 Cov.: 33 AF XY: 0.412 AC XY: 30641 AN XY: 74330

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.388

Alfa AF: 0.354 Hom.: 1384

Bravo AF: 0.436

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7660345; hg19: chr4-187921499;