rs1891284

Variant names:

• chr6-14651937-C-T
• rs1891284
• ENST00000702111.1:n.37+4846G>A

Variant summary

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

The ENST00000702111.1(ENSG00000234261):​n.37+4846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,030 control chromosomes in the GnomAD database, including 12,634 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 0.39 (12634 hom., cov: 32)
• Consequence: ENSG00000234261 ENST00000702111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 5 publications found

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702111.1. 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
	ENSG00000234261	ENST00000702111.1		n.37+4846G>A		intron	N/A
	ENSG00000234261	ENST00000729738.1		n.111-7868G>A		intron	N/A
	ENSG00000234261	ENST00000729739.1		n.47-7868G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59856 AN: 151912 Hom.: 12622 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.394 AC: 59896 AN: 152030 Hom.: 12634 Cov.: 32 AF XY: 0.395 AC XY: 29333 AN XY: 74318

African (AFR) AF: 0.239 AC: 9910 AN: 41442

American (AMR) AF: 0.526 AC: 8032 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1535 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2414 AN: 5164

South Asian (SAS) AF: 0.446 AC: 2153 AN: 4824

European-Finnish (FIN) AF: 0.367 AC: 3879 AN: 10564

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30532 AN: 67972

Other (OTH) AF: 0.448 AC: 946 AN: 2110

Alfa AF: 0.440 Hom.: 12190

Bravo AF: 0.399

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.89
DANN	Benign	0.73
PhyloP100		-0.20

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: rs1891284;

hg19: chr6-14652168;