rs6572915

chr14-53587721-A-G

Variant summary

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

The ENST00000648066.1(ENSG00000237356):n.335-99478A>G 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 0.343 in 151,998 control chromosomes in the GnomAD database, including 9,020 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 0.34 (9020 hom., cov: 31)
• Consequence: ENST00000648066.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370504	XR_943876.3	n.29701-99478A>G		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750974.1	n.3896-99478A>G		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750975.3	n.29701-99478A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648066.1	n.335-99478A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52035 AN: 151880 Hom.: 8997 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.343 AC: 52100 AN: 151998 Hom.: 9020 Cov.: 31 AF XY: 0.340 AC XY: 25243 AN XY: 74316

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.324

Alfa AF: 0.334 Hom.: 1074

Bravo AF: 0.349

Asia WGS AF: 0.338 AC: 1175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.077
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6572915; hg19: chr14-54054439;