rs305087

Variant names:

• chr16-85948640-T-C
• rs305087
• ENST00000645383.1:n.1026T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645383.1(ENSG00000285163):​n.1026T>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: ENSG00000285163 ENST00000645383.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 6 publications found

Genes affected

ENSG00000285163 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105371388	XR_001752395.1	n.674T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285163	ENST00000645383.1	n.1026T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000285163	ENST00000646214.1	n.710T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000285163	ENST00000646986.2	n.1348T>C		non_coding_transcript_exon_variant	Exon 4 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.156 AC: 5 AN: 32

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.395 AC: 16352 AN: 41442

American (AMR) AF: 0.133 AC: 2029 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1237 AN: 5154

South Asian (SAS) AF: 0.236 AC: 1136 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1904 AN: 10592

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11803 AN: 67986

Other (OTH) AF: 0.210 AC: 443 AN: 2112

Alfa AF: 0.184 Hom.: 5019

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs305087; hg19: chr16-85982246;