rs1126179

Positions:

• chr16-65861461-A-G
• chr16-65861461-A-T

Variant summary

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

The ENST00000568767.1(ENSG00000260695):​n.2324T>C 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 0.571 in 152,154 control chromosomes in the GnomAD database, including 25,389 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 0.57 (25387 hom., cov: 33)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: ENSG00000260695 ENST00000568767.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

ENSG00000260695 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.65861461A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000260695	ENST00000568767.1	n.2324T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86883 AN: 152032 Hom.: 25385 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.609

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.571 AC: 86921 AN: 152150 Hom.: 25387 Cov.: 33 AF XY: 0.577 AC XY: 42918 AN XY: 74380

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.607

Alfa AF: 0.589 Hom.: 15025

Bravo AF: 0.566

Asia WGS AF: 0.721 AC: 2509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.83
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1126179; hg19: chr16-65895364;