6-43837071-G-C

Variant names:

• chr6-43837071-G-C
• rs2396083
• ENST00000637813.1:n.366-5440G>C

Variant summary

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

The ENST00000637813.1(ENSG00000283573):​n.366-5440G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,028 control chromosomes in the GnomAD database, including 29,625 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 0.60 (29625 hom., cov: 31)
• Consequence: ENSG00000283573 ENST00000637813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375069	XR_001744130.1	n.676-60C>G		intron_variant	Intron 2 of 2
LOC105375070	XR_007059588.1	n.193-5440G>C		intron_variant	Intron 1 of 2
LOC105375070	XR_007059589.1	n.193-5440G>C		intron_variant	Intron 1 of 2
LOC105375069	XR_007059590.1	n.393-60C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283573	ENST00000637813.1	n.366-5440G>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90948 AN: 151910 Hom.: 29620 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.598 AC: 90984 AN: 152028 Hom.: 29625 Cov.: 31 AF XY: 0.603 AC XY: 44807 AN XY: 74304

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.617

Alfa AF: 0.521 Hom.: 1661

Bravo AF: 0.588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2396083; hg19: chr6-43804808;