rs11868324

Variant names:

• chr17-63499948-A-G
• rs11868324
• ENST00000577647.2:n.1969+2963A>G

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.1969+2963A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,070 control chromosomes in the GnomAD database, including 30,978 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 0.62 (30978 hom., cov: 32)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 5 publications found

Genes affected

ENSG00000264813 (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 = 0.85 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
ENSG00000264813	ENST00000577647.2	n.1969+2963A>G		intron_variant	Intron 13 of 30	2		ENSP00000464149.1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94043 AN: 151950 Hom.: 30895 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.619 AC: 94189 AN: 152070 Hom.: 30978 Cov.: 32 AF XY: 0.617 AC XY: 45896 AN XY: 74336

African (AFR) AF: 0.858 AC: 35629 AN: 41534

American (AMR) AF: 0.597 AC: 9120 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3010 AN: 5160

South Asian (SAS) AF: 0.651 AC: 3134 AN: 4814

European-Finnish (FIN) AF: 0.497 AC: 5250 AN: 10558

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35010 AN: 67936

Other (OTH) AF: 0.558 AC: 1177 AN: 2108

Alfa AF: 0.611 Hom.: 4301

Bravo AF: 0.633

Asia WGS AF: 0.690 AC: 2396 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	3.4
DANN	Benign	0.30
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11868324; hg19: chr17-61577309;