chr2-150790358-G-C

Variant names:

• chr2-150790358-G-C
• rs1010330
• ENST00000728638.1:n.144+3031G>C

Variant summary

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

The ENST00000728638.1(ENSG00000295210):​n.144+3031G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 141,964 control chromosomes in the GnomAD database, including 39,912 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 0.77 (39912 hom., cov: 27)
• Consequence: ENSG00000295210 ENST00000728638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 publications found

Genes affected

ENSG00000295210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.796 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
ENSG00000295210	ENST00000728638.1	n.144+3031G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.769 AC: 109054 AN: 141884 Hom.: 39891 Cov.: 27

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.769 AC: 109114 AN: 141964 Hom.: 39912 Cov.: 27 AF XY: 0.767 AC XY: 52881 AN XY: 68914

African (AFR) AF: 0.723 AC: 27453 AN: 37982

American (AMR) AF: 0.808 AC: 11689 AN: 14462

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2699 AN: 3374

East Asian (EAS) AF: 0.774 AC: 3797 AN: 4904

South Asian (SAS) AF: 0.774 AC: 3418 AN: 4414

European-Finnish (FIN) AF: 0.758 AC: 6637 AN: 8754

Middle Eastern (MID) AF: 0.770 AC: 211 AN: 274

European-Non Finnish (NFE) AF: 0.785 AC: 50948 AN: 64932

Other (OTH) AF: 0.760 AC: 1497 AN: 1970

Alfa AF: 0.653 Hom.: 1905

Bravo AF: 0.731

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.44
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1010330; hg19: chr2-151646872;