rs535255

Variant names:

• chr16-995838-T-C
• rs535255
• ENST00000565401.3:n.1091A>G

Variant summary

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

The ENST00000565401.3(ENSG00000260496):​n.1091A>G 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 0.179 in 152,142 control chromosomes in the GnomAD database, including 3,106 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 0.18 (3106 hom., cov: 32)
• Consequence: ENSG00000260496 ENST00000565401.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 9 publications found

Genes affected

ENSG00000260496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565401.3. 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
	ENSG00000260496	ENST00000565401.3	TSL:4	n.1091A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27130 AN: 152024 Hom.: 3099 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.172

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.179 AC: 27169 AN: 152142 Hom.: 3106 Cov.: 32 AF XY: 0.174 AC XY: 12939 AN XY: 74376

African (AFR) AF: 0.317 AC: 13144 AN: 41456

American (AMR) AF: 0.123 AC: 1877 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5182

South Asian (SAS) AF: 0.151 AC: 727 AN: 4822

European-Finnish (FIN) AF: 0.0657 AC: 697 AN: 10602

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9531 AN: 68004

Other (OTH) AF: 0.173 AC: 367 AN: 2116

Alfa AF: 0.154 Hom.: 1777

Bravo AF: 0.191

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.64
PhyloP100		-0.28

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: rs535255;

hg19: chr16-1045838;

COSMIC: COSV73794243;