chr2-1554155-T-C

Variant names:

• chr2-1554155-T-C
• rs10206020
• ENST00000438247.1:n.516-7220A>G

Variant summary

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

The ENST00000438247.1(ENSG00000228613):​n.516-7220A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,044 control chromosomes in the GnomAD database, including 6,256 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 0.27 (6256 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000228613 ENST00000438247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 10 publications found

Genes affected

ENSG00000228613 (HGNC:58132):

ENSG00000283766 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723730	NR_168373.1	n.746-15T>C		intron_variant	Intron 2 of 2
LALTOP	NR_198948.1	n.3004-7220A>G		intron_variant	Intron 4 of 6
LALTOP	NR_198949.1	n.3004-7220A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228613	ENST00000438247.1	n.516-7220A>G		intron_variant	Intron 2 of 2	4
ENSG00000283766	ENST00000640435.1	n.231-15T>C		intron_variant	Intron 2 of 2	5
ENSG00000231482	ENST00000650512.1	n.547+26046A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40670 AN: 151926 Hom.: 6231 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.230

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.268 AC: 40760 AN: 152044 Hom.: 6256 Cov.: 33 AF XY: 0.268 AC XY: 19949 AN XY: 74318

African (AFR) AF: 0.427 AC: 17691 AN: 41434

American (AMR) AF: 0.223 AC: 3416 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3470

East Asian (EAS) AF: 0.183 AC: 946 AN: 5170

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4814

European-Finnish (FIN) AF: 0.256 AC: 2709 AN: 10574

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13644 AN: 67976

Other (OTH) AF: 0.236 AC: 498 AN: 2112

Alfa AF: 0.278 Hom.: 3855

Bravo AF: 0.272

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs10206020; hg19: chr2-1557927;