14-63147738-T-C

Variant names:

• chr14-63147738-T-C
• rs7401404
• ENST00000654636.1:n.401+10636A>G

Variant summary

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

The ENST00000654636.1(ENSG00000259093):​n.401+10636A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,010 control chromosomes in the GnomAD database, including 29,410 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 0.62 (29410 hom., cov: 32)
• Consequence: ENSG00000259093 ENST00000654636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 4 publications found

Genes affected

ENSG00000259093 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654636.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259093	ENST00000654636.1		n.401+10636A>G		intron	N/A
	ENSG00000259093	ENST00000737109.1		n.625+10636A>G		intron	N/A
	ENSG00000259093	ENST00000737110.1		n.265-19527A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93550 AN: 151892 Hom.: 29405 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.616 AC: 93595 AN: 152010 Hom.: 29410 Cov.: 32 AF XY: 0.620 AC XY: 46075 AN XY: 74270

African (AFR) AF: 0.480 AC: 19901 AN: 41456

American (AMR) AF: 0.678 AC: 10359 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2144 AN: 3468

East Asian (EAS) AF: 0.518 AC: 2674 AN: 5164

South Asian (SAS) AF: 0.699 AC: 3363 AN: 4814

European-Finnish (FIN) AF: 0.735 AC: 7774 AN: 10572

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45257 AN: 67946

Other (OTH) AF: 0.606 AC: 1279 AN: 2112

Alfa AF: 0.641 Hom.: 85088

Bravo AF: 0.603

Asia WGS AF: 0.572 AC: 1990 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	1.3
DANN	Benign	0.25
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7401404; hg19: chr14-63614456;