chr2-16363695-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425176.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224400	ENST00000425176.6	TSL:3	n.81+9395C>G		intron	N/A
	ENSG00000224400	ENST00000427950.1	TSL:3	n.83+8428C>G		intron	N/A
	ENSG00000224400	ENST00000766117.1		n.73+9395C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6531074;

hg19: chr2-16544963;