1-168619944-T-G

Variant names:

• chr1-168619944-T-G
• rs2419117
• ENST00000823814.1:n.129+21205A>C

Variant summary

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

The ENST00000823814.1(ENSG00000307090):​n.129+21205A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,076 control chromosomes in the GnomAD database, including 15,091 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 0.44 (15091 hom., cov: 33)
• Consequence: ENSG00000307090 ENST00000823814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 3 publications found

Genes affected

ENSG00000307090 (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 (EAS) allele frequency at 95% confidence interval = 0.7 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
ENSG00000307090	ENST00000823814.1	n.129+21205A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66558 AN: 151958 Hom.: 15065 Cov.: 33

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.438 AC: 66613 AN: 152076 Hom.: 15091 Cov.: 33 AF XY: 0.446 AC XY: 33169 AN XY: 74350

African (AFR) AF: 0.441 AC: 18310 AN: 41490

American (AMR) AF: 0.509 AC: 7785 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1325 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3725 AN: 5180

South Asian (SAS) AF: 0.484 AC: 2339 AN: 4828

European-Finnish (FIN) AF: 0.507 AC: 5342 AN: 10540

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26515 AN: 67954

Other (OTH) AF: 0.404 AC: 854 AN: 2114

Alfa AF: 0.388 Hom.: 6596

Bravo AF: 0.440

Asia WGS AF: 0.553 AC: 1924 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	5.8
DANN	Benign	0.55
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs2419117; hg19: chr1-168589182;