2-221292957-G-T

Variant names:

• chr2-221292957-G-T
• rs10498105
• ENST00000702411.2:n.376-4452C>A

Variant summary

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

The ENST00000702411.2(ENSG00000290000):​n.376-4452C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,998 control chromosomes in the GnomAD database, including 5,987 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 0.25 (5987 hom., cov: 32)
• Consequence: ENSG00000290000 ENST00000702411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 2 publications found

Genes affected

ENSG00000290000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702411.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290000	ENST00000702411.2		n.376-4452C>A		intron	N/A
	ENSG00000290000	ENST00000798102.1		n.229-4452C>A		intron	N/A
	ENSG00000290000	ENST00000798103.1		n.90-4452C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38351 AN: 151880 Hom.: 5990 Cov.: 32

Gnomad AFR AF: 0.0595

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.252 AC: 38336 AN: 151998 Hom.: 5987 Cov.: 32 AF XY: 0.259 AC XY: 19209 AN XY: 74282

African (AFR) AF: 0.0594 AC: 2464 AN: 41466

American (AMR) AF: 0.256 AC: 3917 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3466

East Asian (EAS) AF: 0.269 AC: 1390 AN: 5160

South Asian (SAS) AF: 0.351 AC: 1693 AN: 4822

European-Finnish (FIN) AF: 0.420 AC: 4432 AN: 10544

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.333 AC: 22608 AN: 67950

Other (OTH) AF: 0.237 AC: 499 AN: 2108

Alfa AF: 0.297 Hom.: 3712

Bravo AF: 0.230

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.069
DANN	Benign	0.47
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10498105;

hg19: chr2-222157677;