16-65861461-A-G

Variant names:

• chr16-65861461-A-G
• rs1126179
• ENST00000568767.1:n.2324T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000260695 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260695	ENST00000568767.1	n.2324T>C		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.453 AC: 18808 AN: 41498

American (AMR) AF: 0.640 AC: 9784 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2102 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4276 AN: 5180

South Asian (SAS) AF: 0.651 AC: 3137 AN: 4816

European-Finnish (FIN) AF: 0.643 AC: 6804 AN: 10584

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39968 AN: 68002

Other (OTH) AF: 0.607 AC: 1281 AN: 2110

Alfa AF: 0.588 Hom.: 16384

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1126179; hg19: chr16-65895364;