rs11987678

Variant names:

• chr8-80316591-T-C
• rs11987678
• ENST00000522044.1:n.405-23210T>C

Variant summary

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

The ENST00000522044.1(ENSG00000253238):​n.405-23210T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,068 control chromosomes in the GnomAD database, including 2,933 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 0.14 (2933 hom., cov: 32)
• Consequence: ENSG00000253238 ENST00000522044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

ENSG00000253238 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 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
ENSG00000253238	ENST00000522044.1	n.405-23210T>C		intron_variant	Intron 3 of 3	3
ENSG00000253238	ENST00000644465.1	n.253+27589T>C		intron_variant	Intron 2 of 4
ENSG00000253238	ENST00000656068.1	n.392-19457T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20698 AN: 151950 Hom.: 2911 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0840

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0473

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.137 AC: 20761 AN: 152068 Hom.: 2933 Cov.: 32 AF XY: 0.134 AC XY: 9953 AN XY: 74378

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.0837

Gnomad4 ASJ AF: 0.0868

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0433

Gnomad4 NFE AF: 0.0474

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0697 Hom.: 435

Bravo AF: 0.150

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11987678; hg19: chr8-81228826;