rs6842739

Positions:

• chr4-59623792-A-G
• chr4-59623792-A-T

Variant summary

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

The ENST00000504537.1(ENSG00000249392):​n.114+6419T>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 0.637 in 152,002 control chromosomes in the GnomAD database, including 31,558 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 0.64 (31558 hom., cov: 32)
• Consequence: ENST00000504537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504537.1	n.114+6419T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96723 AN: 151884 Hom.: 31544 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.637 AC: 96771 AN: 152002 Hom.: 31558 Cov.: 32 AF XY: 0.636 AC XY: 47242 AN XY: 74284

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.647

Alfa AF: 0.695 Hom.: 74702

Bravo AF: 0.636

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6842739; hg19: chr4-60489510;