chr4-104309490-A-C

Position:

• chr4-104309490-A-C

Variant summary

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

The ENST00000514327.5(ENSG00000251170):​n.163-22733A>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 0.454 in 152,008 control chromosomes in the GnomAD database, including 17,172 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 0.45 (17172 hom., cov: 33)
• Consequence: ENST00000514327.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377350	XR_939033.3	n.236-25999T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000514327.5	n.163-22733A>C		intron_variant, non_coding_transcript_variant		4
	ENST00000505680.1	n.57-21912A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68926 AN: 151890 Hom.: 17159 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.454 AC: 68961 AN: 152008 Hom.: 17172 Cov.: 33 AF XY: 0.458 AC XY: 34047 AN XY: 74272

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.480

Alfa AF: 0.504 Hom.: 8346

Bravo AF: 0.457

Asia WGS AF: 0.662 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs960345; hg19: chr4-105230647;