chr6-14597751-C-T

Variant names:

• chr6-14597751-C-T
• rs9296949
• ENST00000414740.2:n.61-152G>A

Variant summary

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

The ENST00000414740.2(ENSG00000234261):​n.61-152G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0546 in 152,128 control chromosomes in the GnomAD database, including 396 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 0.055 (396 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000414740.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 4 publications found

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928354	XR_001743992.2	n.362-152G>A		intron_variant	Intron 4 of 4
LOC101928354	XR_007059472.1	n.284-152G>A		intron_variant	Intron 3 of 3
LOC101928354	XR_241980.4	n.224-152G>A		intron_variant	Intron 3 of 3
LOC101928354	XR_926516.3	n.187-152G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234261	ENST00000414740.2	n.61-152G>A		intron_variant	Intron 1 of 1	5
ENSG00000234261	ENST00000729738.1	n.288-152G>A		intron_variant	Intron 3 of 7
ENSG00000234261	ENST00000729739.1	n.224-152G>A		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 8288 AN: 152010 Hom.: 393 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0546 AC: 8302 AN: 152128 Hom.: 396 Cov.: 32 AF XY: 0.0575 AC XY: 4276 AN XY: 74376

African (AFR) AF: 0.0104 AC: 431 AN: 41498

American (AMR) AF: 0.104 AC: 1594 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1090 AN: 5176

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4818

European-Finnish (FIN) AF: 0.0512 AC: 542 AN: 10580

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0545 AC: 3703 AN: 67982

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0538 Hom.: 46

Bravo AF: 0.0591

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.38
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs9296949; hg19: chr6-14597982;