chr1-5304574-C-T

Position:

• chr1-5304574-C-T

Variant summary

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

The ENST00000641871.1(ENSG00000284616):​n.909G>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 0.624 in 151,982 control chromosomes in the GnomAD database, including 29,845 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 0.62 (29844 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: ENST00000641871.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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
	ENST00000641871.1	n.909G>A		non_coding_transcript_exon_variant	2/4

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94764 AN: 151860 Hom.: 29801 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.612

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.624 AC: 94861 AN: 151978 Hom.: 29844 Cov.: 32 AF XY: 0.628 AC XY: 46662 AN XY: 74266

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.614

Alfa AF: 0.602 Hom.: 6371

Bravo AF: 0.618

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9439519; hg19: chr1-5364634;