ENST00000827601.1:n.407-9929C>T

Variant names:

• chr14-60621022-G-A
• rs7156317
• ENST00000827601.1:n.407-9929C>T

Variant summary

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

The ENST00000827601.1(ENSG00000307639):​n.407-9929C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,198 control chromosomes in the GnomAD database, including 53,608 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 0.83 (53608 hom., cov: 32)
• Consequence: ENSG00000307639 ENST00000827601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 8 publications found

Genes affected

ENSG00000307639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 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
ENSG00000307639	ENST00000827601.1	n.407-9929C>T		intron_variant	Intron 2 of 3
ENSG00000307639	ENST00000827602.1	n.404+20541C>T		intron_variant	Intron 2 of 2
ENSG00000307639	ENST00000827603.1	n.401-9929C>T		intron_variant	Intron 2 of 3
ENSG00000307639	ENST00000827604.1	n.681-6850C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126401 AN: 152080 Hom.: 53591 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.831 AC: 126457 AN: 152198 Hom.: 53608 Cov.: 32 AF XY: 0.833 AC XY: 61954 AN XY: 74406

African (AFR) AF: 0.654 AC: 27120 AN: 41486

American (AMR) AF: 0.883 AC: 13508 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3061 AN: 3468

East Asian (EAS) AF: 0.850 AC: 4409 AN: 5186

South Asian (SAS) AF: 0.730 AC: 3508 AN: 4806

European-Finnish (FIN) AF: 0.968 AC: 10275 AN: 10612

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61761 AN: 68024

Other (OTH) AF: 0.829 AC: 1752 AN: 2114

Alfa AF: 0.888 Hom.: 27426

Bravo AF: 0.820

Asia WGS AF: 0.782 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.52
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs7156317; hg19: chr14-61087740;