rs6869841

Variant names:

• chr5-173512423-C-T
• rs6869841
• ENST00000827042.1:n.446+6051C>T

Variant summary

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

The ENST00000827042.1(ENSG00000253968):​n.446+6051C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,142 control chromosomes in the GnomAD database, including 5,345 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 0.25 (5345 hom., cov: 32)
• Consequence: ENSG00000253968 ENST00000827042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 40 publications found

Genes affected

ENSG00000253968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377732	XR_001743001.1	n.3056+4833C>T		intron_variant	Intron 14 of 14
LOC105377732	XR_007059057.1	n.4116+4833C>T		intron_variant	Intron 17 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253968	ENST00000827042.1	n.446+6051C>T		intron_variant	Intron 2 of 2
ENSG00000253968	ENST00000827044.1	n.374+6051C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38714 AN: 152024 Hom.: 5338 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.255 AC: 38751 AN: 152142 Hom.: 5345 Cov.: 32 AF XY: 0.252 AC XY: 18720 AN XY: 74386

African (AFR) AF: 0.365 AC: 15157 AN: 41484

American (AMR) AF: 0.195 AC: 2984 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3472

East Asian (EAS) AF: 0.180 AC: 933 AN: 5182

South Asian (SAS) AF: 0.289 AC: 1390 AN: 4818

European-Finnish (FIN) AF: 0.198 AC: 2097 AN: 10586

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14379 AN: 68006

Other (OTH) AF: 0.252 AC: 531 AN: 2110

Alfa AF: 0.226 Hom.: 7231

Bravo AF: 0.258

Asia WGS AF: 0.223 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.40
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6869841; hg19: chr5-172939426;