rs16968477

Variant names:

• chr15-74370046-C-T
• rs16968477
• ENST00000568496.3:n.3852C>T

Variant summary

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

The ENST00000568496.3(ENSG00000261821):​n.3852C>T 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 0.232 in 152,026 control chromosomes in the GnomAD database, including 5,174 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 (5174 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: ENSG00000261821 ENST00000568496.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 12 publications found

Genes affected

ENSG00000261821 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903524	XR_007064709.1	n.4429C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261821	ENST00000568496.3	n.3852C>T		non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000302041	ENST00000783573.1	n.148G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000302041	ENST00000783574.1	n.219G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35130 AN: 151898 Hom.: 5151 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

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: 0.125 AC: 1 AN: 8

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.232 AC: 35214 AN: 152016 Hom.: 5174 Cov.: 32 AF XY: 0.230 AC XY: 17097 AN XY: 74312

African (AFR) AF: 0.411 AC: 16994 AN: 41390

American (AMR) AF: 0.179 AC: 2743 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3468

East Asian (EAS) AF: 0.317 AC: 1644 AN: 5180

South Asian (SAS) AF: 0.324 AC: 1559 AN: 4810

European-Finnish (FIN) AF: 0.126 AC: 1337 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9676 AN: 67980

Other (OTH) AF: 0.216 AC: 456 AN: 2108

Alfa AF: 0.177 Hom.: 9234

Bravo AF: 0.242

Asia WGS AF: 0.381 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.68
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs16968477; hg19: chr15-74662387;