rs1428445

Positions:

• chr5-158568795-G-A
• chr5-158568795-G-C

Variant summary

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

The ENST00000642039.1(ENSG00000254135):​n.705-19661G>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 0.265 in 152,068 control chromosomes in the GnomAD database, including 5,874 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 0.27 (5874 hom., cov: 32)
• Consequence: ENST00000642039.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 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
	ENST00000642039.1	n.705-19661G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40277 AN: 151946 Hom.: 5869 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.265 AC: 40313 AN: 152068 Hom.: 5874 Cov.: 32 AF XY: 0.262 AC XY: 19469 AN XY: 74372

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.262

Alfa AF: 0.233 Hom.: 2165

Bravo AF: 0.280

Asia WGS AF: 0.355 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1428445; hg19: chr5-157995803;