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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568496.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261821	ENST00000568496.3	TSL:2	n.3852C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000302041	ENST00000783573.1		n.148G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000302041	ENST00000783574.1		n.219G>A		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16968477;

hg19: chr15-74662387;