rs2415438

Positions:

• chr14-38108328-A-G
• chr14-38108328-A-T

Variant summary

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

The ENST00000554687.1(ENSG00000259048):​n.200+60012T>C 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 0.678 in 152,020 control chromosomes in the GnomAD database, including 36,159 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 0.68 (36159 hom., cov: 32)
• Consequence: ENST00000554687.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000554687.1	n.200+60012T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102928 AN: 151902 Hom.: 36114 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.678 AC: 103029 AN: 152020 Hom.: 36159 Cov.: 32 AF XY: 0.674 AC XY: 50065 AN XY: 74314

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.663

Alfa AF: 0.618 Hom.: 57111

Bravo AF: 0.690

Asia WGS AF: 0.511 AC: 1770 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2415438; hg19: chr14-38577533;