2-177044867-T-C

Variant names:

• chr2-177044867-T-C
• rs1529093
• ENST00000441205.1:n.370+49708A>G

Variant summary

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

The ENST00000441205.1(ENSG00000229337):​n.370+49708A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,024 control chromosomes in the GnomAD database, including 17,777 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 0.47 (17777 hom., cov: 32)
• Consequence: ENSG00000229337 ENST00000441205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911
• Publications: 12 publications found

Genes affected

ENSG00000229337 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 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
ENSG00000229337	ENST00000441205.1	n.370+49708A>G		intron_variant	Intron 3 of 5	5
ENSG00000229337	ENST00000452002.5	n.45+11405A>G		intron_variant	Intron 1 of 2	4
ENSG00000229337	ENST00000653899.1	n.608-11104A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70772 AN: 151906 Hom.: 17769 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.466 AC: 70801 AN: 152024 Hom.: 17777 Cov.: 32 AF XY: 0.462 AC XY: 34324 AN XY: 74310

African (AFR) AF: 0.275 AC: 11401 AN: 41460

American (AMR) AF: 0.473 AC: 7221 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1796 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2558 AN: 5166

South Asian (SAS) AF: 0.551 AC: 2654 AN: 4818

European-Finnish (FIN) AF: 0.480 AC: 5069 AN: 10558

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38639 AN: 67972

Other (OTH) AF: 0.495 AC: 1046 AN: 2112

Alfa AF: 0.528 Hom.: 76930

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.8
DANN	Benign	0.79
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs1529093; hg19: chr2-177909595;