chr1-166259149-C-T

Position:

• chr1-166259149-C-T

Variant summary

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

The ENST00000653824.2(ENSG00000229588):​n.204-76179C>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 0.879 in 151,902 control chromosomes in the GnomAD database, including 60,010 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 0.88 (60010 hom., cov: 31)
• Consequence: ENST00000653824.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268276	XR_002958633.2	n.179-76179C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653824.2	n.204-76179C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133429 AN: 151784 Hom.: 59995 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.879 AC: 133488 AN: 151902 Hom.: 60010 Cov.: 31 AF XY: 0.876 AC XY: 65053 AN XY: 74246

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.899

Alfa AF: 0.964 Hom.: 111544

Bravo AF: 0.857

Asia WGS AF: 0.889 AC: 3057 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1432120; hg19: chr1-166228386;