chr4-74556361-C-A

Position:

• chr4-74556361-C-A

Variant summary

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

The ENST00000510419.1(ENSG00000249942):​n.374-261G>T 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 0.273 in 152,052 control chromosomes in the GnomAD database, including 6,774 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 0.27 (6774 hom., cov: 33)
• Consequence: ENST00000510419.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986229	XR_001741513.2	n.174-3529G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000510419.1	n.374-261G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41477 AN: 151934 Hom.: 6771 Cov.: 33

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.273 AC: 41493 AN: 152052 Hom.: 6774 Cov.: 33 AF XY: 0.274 AC XY: 20392 AN XY: 74342

Gnomad4 AFR AF: 0.0898

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.270

Alfa AF: 0.292 Hom.: 1178

Bravo AF: 0.271

Asia WGS AF: 0.316 AC: 1100 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11942466; hg19: chr4-75422078;