1-89485214-G-A

Position:

• chr1-89485214-G-A

Variant summary

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

The ENST00000671515.1(ENSG00000286548):​n.317-3351C>T 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 0.176 in 152,030 control chromosomes in the GnomAD database, including 2,944 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 0.18 (2944 hom., cov: 32)
• Consequence: ENST00000671515.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.291 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
	ENST00000671515.1	n.317-3351C>T		intron_variant, non_coding_transcript_variant
	ENST00000662176.1	n.258-3351C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26800 AN: 151914 Hom.: 2940 Cov.: 32

Gnomad AFR AF: 0.0625

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.176 AC: 26807 AN: 152030 Hom.: 2944 Cov.: 32 AF XY: 0.175 AC XY: 13003 AN XY: 74318

Gnomad4 AFR AF: 0.0624

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0213

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.188

Alfa AF: 0.202 Hom.: 427

Bravo AF: 0.181

Asia WGS AF: 0.100 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs975977; hg19: chr1-89950773; COSMIC: COSV59970737;