rs305087

chr16-85948640-T-C

Variant summary

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

The ENST00000646214.1(ENSG00000285163):n.710T>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 0.233 in 152,120 control chromosomes in the GnomAD database, including 5,048 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 0.23 (5047 hom., cov: 32)
  • Exomes 𝑓: 0.18 (1 hom.)
• Consequence: ENST00000646214.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371388	XR_001752395.1	n.674T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646214.1	n.710T>C		non_coding_transcript_exon_variant	4/4
	ENST00000645383.1	n.1026T>C		non_coding_transcript_exon_variant	4/4
	ENST00000646986.1	n.1348T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35436 AN: 151956 Hom.: 5031 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.182 AC: 8 AN: 44 Hom.: 1 Cov.: 0 AF XY: 0.182 AC XY: 4 AN XY: 22

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.233 AC: 35481 AN: 152076 Hom.: 5047 Cov.: 32 AF XY: 0.232 AC XY: 17242 AN XY: 74336

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.210

Alfa AF: 0.179 Hom.: 3447

Bravo AF: 0.233

Asia WGS AF: 0.244 AC: 850 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.086
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs305087; hg19: chr16-85982246;