rs2155220

Variant names:

• chr11-76555128-C-T
• rs2155220
• ENST00000830356.1:n.501+415G>A

Variant summary

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

The ENST00000830356.1(ENSG00000308001):​n.501+415G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,128 control chromosomes in the GnomAD database, including 12,647 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 0.40 (12647 hom., cov: 32)
• Consequence: ENSG00000308001 ENST00000830356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707
• Publications: 10 publications found

Genes affected

ENSG00000308001 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.495 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
ENSG00000308001	ENST00000830356.1	n.501+415G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60999 AN: 152010 Hom.: 12628 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.401 AC: 61041 AN: 152128 Hom.: 12647 Cov.: 32 AF XY: 0.402 AC XY: 29914 AN XY: 74362

African (AFR) AF: 0.318 AC: 13190 AN: 41504

American (AMR) AF: 0.489 AC: 7472 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1974 AN: 5172

South Asian (SAS) AF: 0.512 AC: 2473 AN: 4832

European-Finnish (FIN) AF: 0.387 AC: 4093 AN: 10578

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29380 AN: 67972

Other (OTH) AF: 0.404 AC: 853 AN: 2110

Alfa AF: 0.421 Hom.: 5208

Bravo AF: 0.402

Asia WGS AF: 0.435 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.61
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs2155220; hg19: chr11-76266172;