rs12440824

Positions:

• chr15-47932774-A-G

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.189-59935A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,178 control chromosomes in the GnomAD database, including 2,853 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 0.18 (2853 hom., cov: 32)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+48270A>G		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751517.2	n.142+48270A>G		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.82+17412A>G		intron_variant, non_coding_transcript_variant
LOC124900354	XR_007064618.1	n.143-16582A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000662551.1	n.189-59935A>G		intron_variant, non_coding_transcript_variant
	ENST00000560900.1	n.195+48270A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000664705.1	n.189-59935A>G		intron_variant, non_coding_transcript_variant
	ENST00000665188.1	n.69-59935A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26880 AN: 152060 Hom.: 2848 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.177 AC: 26916 AN: 152178 Hom.: 2853 Cov.: 32 AF XY: 0.178 AC XY: 13262 AN XY: 74414

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.170

Alfa AF: 0.128 Hom.: 1512

Bravo AF: 0.188

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.76
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12440824; hg19: chr15-48224971;