ENST00000804907.1:n.82-958G>A

Variant names:

• chr11-102268172-G-A
• rs2124216
• ENST00000804907.1:n.82-958G>A

Variant summary

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

The ENST00000804907.1(ENSG00000304602):​n.82-958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,912 control chromosomes in the GnomAD database, including 4,445 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 0.24 (4445 hom., cov: 32)
• Consequence: ENSG00000304602 ENST00000804907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.747
• Publications: 5 publications found

Genes affected

ENSG00000304602 (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 (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369460	XR_007062863.1	n.126-958G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304602	ENST00000804907.1	n.82-958G>A		intron_variant	Intron 1 of 3
ENSG00000304602	ENST00000804908.1	n.176+218G>A		intron_variant	Intron 1 of 3
ENSG00000304602	ENST00000804909.1	n.161+218G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35834 AN: 151796 Hom.: 4438 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.236 AC: 35861 AN: 151912 Hom.: 4445 Cov.: 32 AF XY: 0.238 AC XY: 17658 AN XY: 74254

African (AFR) AF: 0.186 AC: 7693 AN: 41438

American (AMR) AF: 0.232 AC: 3546 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1937 AN: 5140

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4808

European-Finnish (FIN) AF: 0.280 AC: 2958 AN: 10554

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17220 AN: 67940

Other (OTH) AF: 0.220 AC: 463 AN: 2108

Alfa AF: 0.227 Hom.: 2484

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.76
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs2124216; hg19: chr11-102138903;