rs6890853

Variant names:

• chr5-35852209-G-A
• rs6890853
• ENST00000736912.1:n.55+2111C>T

Variant summary

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

The ENST00000736912.1(ENSG00000248969):​n.55+2111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,180 control chromosomes in the GnomAD database, including 4,948 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 0.25 (4948 hom., cov: 33)
• Consequence: ENSG00000248969 ENST00000736912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 26 publications found

Genes affected

ENSG00000248969 (HGNC:59028):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736912.1. 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
	ENSG00000248969	ENST00000736912.1		n.55+2111C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37994 AN: 152062 Hom.: 4948 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.250 AC: 38020 AN: 152180 Hom.: 4948 Cov.: 33 AF XY: 0.252 AC XY: 18737 AN XY: 74392

African (AFR) AF: 0.216 AC: 8987 AN: 41556

American (AMR) AF: 0.189 AC: 2887 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1178 AN: 5162

South Asian (SAS) AF: 0.254 AC: 1223 AN: 4822

European-Finnish (FIN) AF: 0.346 AC: 3660 AN: 10578

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18427 AN: 67982

Other (OTH) AF: 0.219 AC: 460 AN: 2100

Alfa AF: 0.260 Hom.: 8458

Bravo AF: 0.236

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.49
PhyloP100		-1.5
PromoterAI		-0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6890853; hg19: chr5-35852311;