rs535255

Positions:

• chr16-995838-T-C

Variant summary

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

The ENST00000565401.2(ENSG00000260496):​n.1084A>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: ENST00000565401.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000565401.2	n.1084A>G		non_coding_transcript_exon_variant	2/2	4

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

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0657

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.173

Alfa AF: 0.153 Hom.: 1037

Bravo AF: 0.191

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs535255; hg19: chr16-1045838; COSMIC: COSV73794243;