2-16363695-C-G

Variant names:

• chr2-16363695-C-G
• rs6531074
• ENST00000425176.6:n.81+9395C>G

Variant summary

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

The ENST00000425176.6(ENSG00000224400):​n.81+9395C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,044 control chromosomes in the GnomAD database, including 44,433 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 0.76 (44433 hom., cov: 32)
• Consequence: ENSG00000224400 ENST00000425176.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 5 publications found

Genes affected

ENSG00000224400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985855	XR_001739298.1	n.276+8428C>G		intron_variant	Intron 1 of 2
LOC107985855	XR_001739299.1	n.276+8428C>G		intron_variant	Intron 1 of 2
LOC107985855	XR_001739300.1	n.276+8428C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224400	ENST00000425176.6	n.81+9395C>G		intron_variant	Intron 1 of 2	3
ENSG00000224400	ENST00000427950.1	n.83+8428C>G		intron_variant	Intron 1 of 3	3
ENSG00000224400	ENST00000766117.1	n.73+9395C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115934 AN: 151926 Hom.: 44384 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.763 AC: 116038 AN: 152044 Hom.: 44433 Cov.: 32 AF XY: 0.761 AC XY: 56561 AN XY: 74298

African (AFR) AF: 0.787 AC: 32656 AN: 41486

American (AMR) AF: 0.710 AC: 10839 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2708 AN: 3466

East Asian (EAS) AF: 0.916 AC: 4715 AN: 5150

South Asian (SAS) AF: 0.870 AC: 4182 AN: 4808

European-Finnish (FIN) AF: 0.687 AC: 7254 AN: 10554

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51116 AN: 67992

Other (OTH) AF: 0.777 AC: 1640 AN: 2112

Alfa AF: 0.750 Hom.: 5332

Bravo AF: 0.763

Asia WGS AF: 0.883 AC: 3070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6531074; hg19: chr2-16544963;