12-5002440-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000256654 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638821.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256654	ENST00000638821.1	TSL:5	n.573-7710G>A		intron	N/A
	ENSG00000256654	ENST00000639005.1	TSL:5	n.685-19248G>A		intron	N/A
	ENSG00000256654	ENST00000640862.1	TSL:5	n.704-20051G>A		intron	N/A

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

African (AFR) AF: 0.126 AC: 5221 AN: 41534

American (AMR) AF: 0.125 AC: 1908 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3472

East Asian (EAS) AF: 0.139 AC: 720 AN: 5182

South Asian (SAS) AF: 0.110 AC: 530 AN: 4820

European-Finnish (FIN) AF: 0.181 AC: 1918 AN: 10588

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12948 AN: 68006

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.180 Hom.: 6786

Bravo AF: 0.156

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.014
DANN	Benign	0.59
PhyloP100		-5.2

Splicing

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

Other links and lift over

dbSNP: rs11063455; hg19: chr12-5111606;