chr1-165708436-C-T

Position:

• chr1-165708436-C-T

Variant summary

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

The ENST00000453762.1(ENSG00000215838):​n.154C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 215,150 control chromosomes in the GnomAD database, including 1,964 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 0.079 (1338 hom., cov: 31)
  • Exomes 𝑓: 0.090 (626 hom.)
• Consequence: ENST00000453762.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC440700	NR_036683.1	n.408-139C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000453762.1	n.154C>T		non_coding_transcript_exon_variant	1/2
	ENST00000400982.2	n.408-139C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11956 AN: 152064 Hom.: 1336 Cov.: 31

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.0779

GnomAD4 exome AF: 0.0904 AC: 5691 AN: 62968 Hom.: 626 Cov.: 0 AF XY: 0.0889 AC XY: 3156 AN XY: 35508

Gnomad4 AFR exome AF: 0.0392

Gnomad4 AMR exome AF: 0.174

Gnomad4 ASJ exome AF: 0.0462

Gnomad4 EAS exome AF: 0.605

Gnomad4 SAS exome AF: 0.104

Gnomad4 FIN exome AF: 0.0810

Gnomad4 NFE exome AF: 0.0480

Gnomad4 OTH exome AF: 0.0750

GnomAD4 genome AF: 0.0786 AC: 11958 AN: 152182 Hom.: 1338 Cov.: 31 AF XY: 0.0832 AC XY: 6188 AN XY: 74382

Gnomad4 AFR AF: 0.0407

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.0522

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0606 Hom.: 578

Bravo AF: 0.0829

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	14
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12027066; hg19: chr1-165677673; COSMIC: COSV68953257;