chr4-59627043-T-C

Position:

• chr4-59627043-T-C

Variant summary

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

The ENST00000504537.1(ENSG00000249392):​n.114+3168A>G 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 0.617 in 151,840 control chromosomes in the GnomAD database, including 30,157 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 0.62 (30157 hom., cov: 30)
• Consequence: ENST00000504537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 (AMR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000504537.1	n.114+3168A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93612 AN: 151722 Hom.: 30157 Cov.: 30

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.617 AC: 93626 AN: 151840 Hom.: 30157 Cov.: 30 AF XY: 0.616 AC XY: 45736 AN XY: 74200

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.630

Alfa AF: 0.665 Hom.: 8800

Bravo AF: 0.614

Asia WGS AF: 0.594 AC: 2067 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	4.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10866168; hg19: chr4-60492761;