rs7144649

Variant names:

• chr14-57355498-G-A
• rs7144649
• ENST00000556602.1:n.53G>A

Variant summary

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

The ENST00000556602.1(ENSG00000259008):​n.53G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 152,062 control chromosomes in the GnomAD database, including 32,434 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 0.60 (32433 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000259008 ENST00000556602.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

ENSG00000259008 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 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
ENSG00000259008	ENST00000556602.1	n.53G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91625 AN: 151942 Hom.: 32449 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.634

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.602 AC: 91607 AN: 152060 Hom.: 32433 Cov.: 32 AF XY: 0.607 AC XY: 45127 AN XY: 74326

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.632

Alfa AF: 0.731 Hom.: 56782

Bravo AF: 0.574

Asia WGS AF: 0.628 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7144649; hg19: chr14-57822216;