rs11063455

Variant names:

• chr12-5002440-G-A
• rs11063455
• ENST00000638821.1:n.573-7710G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-5002440-G-A
• chr12-5002440-G-T

Variant summary

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

The ENST00000638821.1(ENSG00000256654):​n.573-7710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,204 control chromosomes in the GnomAD database, including 2,048 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 (2048 hom., cov: 32)
• Consequence: ENSG00000256654 ENST00000638821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.18

Genes affected

ENSG00000256654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 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
ENSG00000256654	ENST00000638821.1	n.573-7710G>A		intron_variant	Intron 1 of 1	5
ENSG00000256654	ENST00000639005.1	n.685-19248G>A		intron_variant	Intron 2 of 5	5
ENSG00000256654	ENST00000640862.1	n.704-20051G>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24391 AN: 152084 Hom.: 2038 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.161 AC: 24430 AN: 152204 Hom.: 2048 Cov.: 32 AF XY: 0.158 AC XY: 11742 AN XY: 74414

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.173

Alfa AF: 0.183 Hom.: 2704

Bravo AF: 0.156

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.014
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11063455; hg19: chr12-5111606;