ENST00000835438.1:n.500+2554A>G

Variant names:

• chr16-24520397-T-C
• rs11643520
• ENST00000835438.1:n.500+2554A>G

Variant summary

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

The ENST00000835438.1(ENSG00000308621):​n.500+2554A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,200 control chromosomes in the GnomAD database, including 654 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 0.078 (654 hom., cov: 32)
• Consequence: ENSG00000308621 ENST00000835438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 9 publications found

Genes affected

ENSG00000308621 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 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
ENSG00000308621	ENST00000835438.1	n.500+2554A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11803 AN: 152082 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.0192

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0750

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

GnomAD4 genome AF: 0.0775 AC: 11797 AN: 152200 Hom.: 654 Cov.: 32 AF XY: 0.0761 AC XY: 5659 AN XY: 74410

African (AFR) AF: 0.0191 AC: 794 AN: 41546

American (AMR) AF: 0.103 AC: 1568 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3468

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5180

South Asian (SAS) AF: 0.156 AC: 752 AN: 4820

European-Finnish (FIN) AF: 0.0431 AC: 457 AN: 10614

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7324 AN: 67978

Other (OTH) AF: 0.0743 AC: 157 AN: 2114

Alfa AF: 0.104 Hom.: 2144

Bravo AF: 0.0760

Asia WGS AF: 0.0640 AC: 222 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	0.46
DANN	Benign	0.67
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs11643520; hg19: chr16-24531718;