chr4-74554070-A-G

Position:

• chr4-74554070-A-G

Variant summary

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

The ENST00000510419.1(ENSG00000249942):​n.484-1238T>C 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 0.297 in 152,060 control chromosomes in the GnomAD database, including 6,888 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 0.30 (6888 hom., cov: 32)
• Consequence: ENST00000510419.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986229	XR_001741513.2	n.174-1238T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000510419.1	n.484-1238T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45173 AN: 151942 Hom.: 6888 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.297 AC: 45205 AN: 152060 Hom.: 6888 Cov.: 32 AF XY: 0.306 AC XY: 22734 AN XY: 74320

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.287

Alfa AF: 0.288 Hom.: 4545

Bravo AF: 0.291

Asia WGS AF: 0.373 AC: 1294 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10034692; hg19: chr4-75419787;