rs241403

Variant names:

• chr6-32899215-T-C
• rs241403
• ENST00000685247.3:n.884-1705T>C

Variant summary

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

The ENST00000685247.3(ENSG00000289047):​n.884-1705T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,972 control chromosomes in the GnomAD database, including 21,219 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 0.52 (21219 hom., cov: 32)
• Consequence: ENSG00000289047 ENST00000685247.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 18 publications found

Genes affected

ENSG00000289047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100294145	NR_037177.1	n.852-1705T>C		intron_variant	Intron 1 of 1
LOC100294145	NR_037178.1	n.753-1705T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289047	ENST00000685247.3	n.884-1705T>C		intron_variant	Intron 1 of 1
ENSG00000289047	ENST00000701517.2	n.684-1705T>C		intron_variant	Intron 1 of 1
ENSG00000289047	ENST00000753208.1	n.521-1705T>C		intron_variant	Intron 1 of 1
ENSG00000289047	ENST00000753209.1	n.295-1705T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79689 AN: 151854 Hom.: 21194 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.525 AC: 79764 AN: 151972 Hom.: 21219 Cov.: 32 AF XY: 0.524 AC XY: 38955 AN XY: 74286

African (AFR) AF: 0.575 AC: 23826 AN: 41432

American (AMR) AF: 0.473 AC: 7227 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1261 AN: 3468

East Asian (EAS) AF: 0.573 AC: 2961 AN: 5172

South Asian (SAS) AF: 0.532 AC: 2563 AN: 4814

European-Finnish (FIN) AF: 0.528 AC: 5568 AN: 10538

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.510 AC: 34632 AN: 67954

Other (OTH) AF: 0.509 AC: 1071 AN: 2106

Alfa AF: 0.526 Hom.: 6927

Bravo AF: 0.521

Asia WGS AF: 0.564 AC: 1961 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs241403; hg19: chr6-32866992;