rs1224606

Variant names:

• chr15-47853621-T-C
• rs1224606
• ENST00000662551.1:n.188+40705T>C

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+40705T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,144 control chromosomes in the GnomAD database, including 4,269 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 0.16 (4269 hom., cov: 33)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

ENSG00000259754 (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 (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000662551.1	n.188+40705T>C		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.188+40705T>C		intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1	n.68+40705T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24711 AN: 152024 Hom.: 4252 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.163 AC: 24778 AN: 152144 Hom.: 4269 Cov.: 33 AF XY: 0.159 AC XY: 11860 AN XY: 74396

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.0950

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0622

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0680 Hom.: 1056

Bravo AF: 0.176

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1224606; hg19: chr15-48145818;