rs1646066

Variant names:

• chr16-11224649-T-C
• rs1646066
• ENST00000572466.2:n.735T>C

Variant summary

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

The ENST00000572466.2(ENSG00000263033):​n.735T>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 0.194 in 152,202 control chromosomes in the GnomAD database, including 3,483 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 0.19 (3483 hom., cov: 32)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: ENSG00000263033 ENST00000572466.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

Genes affected

ENSG00000263033 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984859	XR_001752080.2	n.1269T>C		non_coding_transcript_exon_variant	Exon 5 of 5
LOC107984859	XR_005647017.2	n.1480T>C		non_coding_transcript_exon_variant	Exon 4 of 4
LOC107984859	XR_005647018.2	n.1321T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC107984859	XR_007064984.1	n.1135T>C		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000263033	ENST00000572466.2	n.735T>C		non_coding_transcript_exon_variant	Exon 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29493 AN: 151978 Hom.: 3463 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.194 AC: 21 AN: 108 Hom.: 0 Cov.: 0 AF XY: 0.222 AC XY: 16 AN XY: 72

Gnomad4 AFR exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.179

Gnomad4 NFE exome AF: 0.207

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.194 AC: 29539 AN: 152094 Hom.: 3483 Cov.: 32 AF XY: 0.199 AC XY: 14798 AN XY: 74334

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.161

Alfa AF: 0.170 Hom.: 1582

Bravo AF: 0.210

Asia WGS AF: 0.355 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.40
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1646066; hg19: chr16-11318506;