6-41682998-C-T

Variant names:

• chr6-41682998-C-T
• rs2842643
• ENST00000844236.1:n.59-97C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000844236.1(ENSG00000309839):​n.59-97C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 151,784 control chromosomes in the GnomAD database, including 43,562 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 0.76 (43562 hom., cov: 31)
• Consequence: ENSG00000309839 ENST00000844236.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 23 publications found

Genes affected

ENSG00000309839 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844236.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309839	ENST00000844236.1		n.59-97C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114521 AN: 151666 Hom.: 43488 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.755 AC: 114654 AN: 151784 Hom.: 43562 Cov.: 31 AF XY: 0.756 AC XY: 56035 AN XY: 74128

African (AFR) AF: 0.839 AC: 34649 AN: 41322

American (AMR) AF: 0.711 AC: 10872 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2375 AN: 3468

East Asian (EAS) AF: 0.754 AC: 3881 AN: 5148

South Asian (SAS) AF: 0.742 AC: 3577 AN: 4818

European-Finnish (FIN) AF: 0.777 AC: 8137 AN: 10468

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48709 AN: 67960

Other (OTH) AF: 0.741 AC: 1566 AN: 2112

Alfa AF: 0.727 Hom.: 177197

Bravo AF: 0.752

Asia WGS AF: 0.779 AC: 2709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2842643; hg19: chr6-41650736;