rs1534837

Positions:

• chr14-79916682-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554307.1(ENSG00000258416):​n.367-23523C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 152,180 control chromosomes in the GnomAD database, including 348 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 0.060 (348 hom., cov: 32)
• Consequence: ENST00000554307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370582	XR_944054.3	n.189+272C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554307.1	n.367-23523C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9189 AN: 152060 Hom.: 348 Cov.: 32

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0604 AC: 9190 AN: 152180 Hom.: 348 Cov.: 32 AF XY: 0.0603 AC XY: 4487 AN XY: 74388

Gnomad4 AFR AF: 0.0268

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0742 Hom.: 220

Bravo AF: 0.0546

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1534837; hg19: chr14-80383025;