chr2-16439169-C-A

Variant names:

• chr2-16439169-C-A
• rs6753768
• ENST00000766117.1:n.148-13033C>A

Variant summary

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

The ENST00000766117.1(ENSG00000224400):​n.148-13033C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,966 control chromosomes in the GnomAD database, including 39,682 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 0.72 (39682 hom., cov: 31)
• Consequence: ENSG00000224400 ENST00000766117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 3 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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
ENSG00000224400	ENST00000766117.1	n.148-13033C>A		intron_variant	Intron 2 of 3
ENSG00000224400	ENST00000766118.1	n.227-13033C>A		intron_variant	Intron 3 of 5
ENSG00000289364	ENST00000766298.1	n.384+30724G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109070 AN: 151848 Hom.: 39652 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.718 AC: 109155 AN: 151966 Hom.: 39682 Cov.: 31 AF XY: 0.722 AC XY: 53621 AN XY: 74246

African (AFR) AF: 0.619 AC: 25674 AN: 41446

American (AMR) AF: 0.746 AC: 11402 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2635 AN: 3470

East Asian (EAS) AF: 0.990 AC: 5092 AN: 5142

South Asian (SAS) AF: 0.812 AC: 3907 AN: 4810

European-Finnish (FIN) AF: 0.730 AC: 7698 AN: 10544

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.740 AC: 50287 AN: 67958

Other (OTH) AF: 0.744 AC: 1571 AN: 2112

Alfa AF: 0.720 Hom.: 6474

Bravo AF: 0.715

Asia WGS AF: 0.873 AC: 3034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.25
DANN	Benign	0.70
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs6753768; hg19: chr2-16620437;