chr1-159372649-C-T

Position:

• chr1-159372649-C-T

Variant summary

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

The ENST00000431862.1(ENSG00000228560):​n.228-8140G>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 0.465 in 152,000 control chromosomes in the GnomAD database, including 20,335 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 0.47 (20335 hom., cov: 32)
• Consequence: ENST00000431862.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 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
	ENST00000431862.1	n.228-8140G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70576 AN: 151882 Hom.: 20288 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.465 AC: 70680 AN: 152000 Hom.: 20335 Cov.: 32 AF XY: 0.464 AC XY: 34458 AN XY: 74278

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.401

Alfa AF: 0.321 Hom.: 17835

Bravo AF: 0.488

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6687840; hg19: chr1-159342439;