2-19745816-T-C

Variant names:

• chr2-19745816-T-C
• rs2123536
• ENST00000810569.1:n.236-1610A>G

Variant summary

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

The ENST00000810569.1(ENSG00000305355):​n.236-1610A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,136 control chromosomes in the GnomAD database, including 53,826 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 0.83 (53826 hom., cov: 33)
• Consequence: ENSG00000305355 ENST00000810569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 27 publications found

Genes affected

ENSG00000305355 (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 (NFE) allele frequency at 95% confidence interval = 0.94 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
ENSG00000305355	ENST00000810569.1	n.236-1610A>G		intron_variant	Intron 2 of 2
ENSG00000305355	ENST00000810570.1	n.398-1610A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126085 AN: 152018 Hom.: 53791 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.917

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.829 AC: 126177 AN: 152136 Hom.: 53826 Cov.: 33 AF XY: 0.825 AC XY: 61352 AN XY: 74380

African (AFR) AF: 0.637 AC: 26402 AN: 41460

American (AMR) AF: 0.781 AC: 11941 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 3367 AN: 3472

East Asian (EAS) AF: 0.647 AC: 3344 AN: 5170

South Asian (SAS) AF: 0.830 AC: 3997 AN: 4814

European-Finnish (FIN) AF: 0.926 AC: 9833 AN: 10614

Middle Eastern (MID) AF: 0.911 AC: 266 AN: 292

European-Non Finnish (NFE) AF: 0.946 AC: 64346 AN: 68008

Other (OTH) AF: 0.845 AC: 1782 AN: 2108

Alfa AF: 0.905 Hom.: 148640

Bravo AF: 0.811

Asia WGS AF: 0.709 AC: 2466 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	0.13
DANN	Benign	0.36
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs2123536; hg19: chr2-19945577;