6-43837071-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637813.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283573	ENST00000637813.1	TSL:4	n.366-5440G>C		intron	N/A
	ENSG00000283573	ENST00000719551.1		n.193-5440G>C		intron	N/A
	ENSG00000294041	ENST00000720677.1		n.332+97G>C		intron	N/A

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

African (AFR) AF: 0.316 AC: 13097 AN: 41432

American (AMR) AF: 0.737 AC: 11264 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2498 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4145 AN: 5180

South Asian (SAS) AF: 0.743 AC: 3576 AN: 4816

European-Finnish (FIN) AF: 0.683 AC: 7222 AN: 10570

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47085 AN: 67954

Other (OTH) AF: 0.617 AC: 1305 AN: 2114

Alfa AF: 0.521 Hom.: 1661

Bravo AF: 0.588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.63
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2396083; hg19: chr6-43804808;