rs1770678

chr1-82299369-T-C

Variant summary

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

The ENST00000650063.1(ENSG00000233290):n.888-83597A>G 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 0.0911 in 152,162 control chromosomes in the GnomAD database, including 839 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 0.091 (839 hom., cov: 32)
• Consequence: ENST00000650063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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
	ENST00000650063.1	n.888-83597A>G		intron_variant, non_coding_transcript_variant
	ENST00000653483.1	n.720-83597A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0908 AC: 13803 AN: 152044 Hom.: 824 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.0911 AC: 13858 AN: 152162 Hom.: 839 Cov.: 32 AF XY: 0.0890 AC XY: 6618 AN XY: 74378

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0502

Gnomad4 SAS AF: 0.0213

Gnomad4 FIN AF: 0.0594

Gnomad4 NFE AF: 0.0609

Gnomad4 OTH AF: 0.0990

Alfa AF: 0.0708 Hom.: 474

Bravo AF: 0.0979

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.94
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1770678; hg19: chr1-82765052;