rs11987678

Variant names:

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

Variant summary

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

Genes affected

ENSG00000253238 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.362 AC: 14974 AN: 41374

American (AMR) AF: 0.0837 AC: 1281 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0868 AC: 301 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4820

European-Finnish (FIN) AF: 0.0433 AC: 459 AN: 10602

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0474 AC: 3220 AN: 68002

Other (OTH) AF: 0.131 AC: 277 AN: 2114

Alfa AF: 0.0712 Hom.: 498

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
PhyloP100		0.0090
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11987678; hg19: chr8-81228826;