1-171090482-G-C

Position:

• chr1-171090482-G-C

Variant summary

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

The ENST00000669750.1(ENSG00000231424):​n.533+77622C>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 0.103 in 152,102 control chromosomes in the GnomAD database, including 1,068 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 0.10 (1068 hom., cov: 32)
• Consequence: ENST00000669750.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 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
	ENST00000669750.1	n.533+77622C>G		intron_variant, non_coding_transcript_variant
	ENST00000653116.1	n.542+77622C>G		intron_variant, non_coding_transcript_variant
	ENST00000664920.1	n.681+31268C>G		intron_variant, non_coding_transcript_variant
	ENST00000670085.1	n.371+77622C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15658 AN: 151984 Hom.: 1060 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0991

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

GnomAD4 genome AF: 0.103 AC: 15684 AN: 152102 Hom.: 1068 Cov.: 32 AF XY: 0.106 AC XY: 7882 AN XY: 74372

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.0495

Gnomad4 NFE AF: 0.0622

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0793 Hom.: 82

Bravo AF: 0.114

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3754491; hg19: chr1-171059623;