rs16928055

Variant names:

• chr11-35892021-T-C
• rs16928055
• XR_007062655.1:n.180T>C

Variant summary

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

The XR_007062655.1(LOC124902661):​n.180T>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 0.103 in 152,266 control chromosomes in the GnomAD database, including 1,103 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 0.10 (1103 hom., cov: 32)
• Consequence: LOC124902661 XR_007062655.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 0 publications found

Genes affected

LOC124902661 (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 (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730429.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254919	ENST00000730429.1		n.264+25990A>G		intron	N/A
	ENSG00000254919	ENST00000730430.1		n.268+25990A>G		intron	N/A
	ENSG00000254919	ENST00000730431.1		n.265+25990A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15614 AN: 152148 Hom.: 1102 Cov.: 32

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.103 AC: 15618 AN: 152266 Hom.: 1103 Cov.: 32 AF XY: 0.106 AC XY: 7860 AN XY: 74440

African (AFR) AF: 0.0241 AC: 1002 AN: 41576

American (AMR) AF: 0.132 AC: 2021 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1283 AN: 5182

South Asian (SAS) AF: 0.212 AC: 1023 AN: 4818

European-Finnish (FIN) AF: 0.104 AC: 1102 AN: 10596

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8121 AN: 68012

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.120 Hom.: 2337

Bravo AF: 0.102

Asia WGS AF: 0.220 AC: 762 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	2.2
DANN	Benign	0.33
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs16928055; hg19: chr11-35913571;