14-65308977-T-G

Variant names:

• chr14-65308977-T-G
• rs11847263
• ENST00000553754.1:n.300+9514A>C

Variant summary

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

The ENST00000553754.1(ENSG00000258760):​n.300+9514A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,914 control chromosomes in the GnomAD database, including 15,062 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 0.43 (15062 hom., cov: 31)
• Consequence: ENSG00000258760 ENST00000553754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 12 publications found

Genes affected

ENSG00000258760 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 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
ENSG00000258760	ENST00000553754.1	n.300+9514A>C		intron_variant	Intron 1 of 2	4
ENSG00000302621	ENST00000788187.1	n.131+20870T>G		intron_variant	Intron 1 of 4
ENSG00000302621	ENST00000788188.1	n.119+20870T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65733 AN: 151796 Hom.: 15041 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.433 AC: 65801 AN: 151914 Hom.: 15062 Cov.: 31 AF XY: 0.444 AC XY: 32953 AN XY: 74220

African (AFR) AF: 0.515 AC: 21319 AN: 41406

American (AMR) AF: 0.428 AC: 6545 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1407 AN: 3464

East Asian (EAS) AF: 0.782 AC: 4031 AN: 5154

South Asian (SAS) AF: 0.541 AC: 2605 AN: 4814

European-Finnish (FIN) AF: 0.458 AC: 4829 AN: 10534

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23762 AN: 67950

Other (OTH) AF: 0.455 AC: 960 AN: 2112

Alfa AF: 0.380 Hom.: 34465

Bravo AF: 0.434

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.55
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11847263; hg19: chr14-65775695;