rs2618221

Variant names:

• chr11-127381999-C-T
• rs2618221
• ENST00000822754.1:n.105+18740C>T

Variant summary

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

The ENST00000822754.1(ENSG00000307024):​n.105+18740C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,146 control chromosomes in the GnomAD database, including 1,959 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 0.15 (1959 hom., cov: 33)
• Consequence: ENSG00000307024 ENST00000822754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 2 publications found

Genes affected

ENSG00000307024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 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
ENSG00000307024	ENST00000822754.1	n.105+18740C>T		intron_variant	Intron 1 of 3
ENSG00000307024	ENST00000822755.1	n.142+18696C>T		intron_variant	Intron 1 of 2
ENSG00000307024	ENST00000822756.1	n.96+18740C>T		intron_variant	Intron 1 of 2
ENSG00000307024	ENST00000822757.1	n.140+18696C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22259 AN: 152028 Hom.: 1953 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0628

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.146 AC: 22268 AN: 152146 Hom.: 1959 Cov.: 33 AF XY: 0.147 AC XY: 10937 AN XY: 74386

African (AFR) AF: 0.234 AC: 9703 AN: 41488

American (AMR) AF: 0.0964 AC: 1476 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3470

East Asian (EAS) AF: 0.170 AC: 876 AN: 5154

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4820

European-Finnish (FIN) AF: 0.102 AC: 1085 AN: 10586

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6919 AN: 68006

Other (OTH) AF: 0.159 AC: 336 AN: 2110

Alfa AF: 0.121 Hom.: 220

Bravo AF: 0.148

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.81
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2618221; hg19: chr11-127251894;