rs1956545

chr14-64386187-C-T

Variant summary

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

The ENST00000641479.1(ENSG00000293482):n.570+1230G>A 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 0.915 in 152,242 control chromosomes in the GnomAD database, including 64,282 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 0.92 (64282 hom., cov: 32)
• Consequence: ENST00000641479.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641479.1	n.570+1230G>A		intron_variant, non_coding_transcript_variant
	ENST00000641725.1	n.465+402G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139239 AN: 152124 Hom.: 64234 Cov.: 32

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.915 AC: 139350 AN: 152242 Hom.: 64282 Cov.: 32 AF XY: 0.912 AC XY: 67895 AN XY: 74430

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.928

Alfa AF: 0.923 Hom.: 51923

Bravo AF: 0.920

Asia WGS AF: 0.735 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.28
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1956545; hg19: chr14-64852905;