rs6941421

Variant names:

• chr6-15088920-T-C
• rs6941421
• ENST00000437648.1:n.228+856A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-15088920-T-C
• chr6-15088920-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000653525.1(ENSG00000234261):​n.139+856A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,964 control chromosomes in the GnomAD database, including 10,777 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 0.37 (10777 hom., cov: 31)
• Consequence: ENSG00000234261 ENST00000653525.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 18 publications found

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653525.1. 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	ENST00000437648.1	TSL:5	n.228+856A>G		intron	N/A
	ENSG00000234261	ENST00000653525.1		n.139+856A>G		intron	N/A
	ENSG00000234261	ENST00000656344.1		n.395+856A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56369 AN: 151844 Hom.: 10773 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.371 AC: 56394 AN: 151964 Hom.: 10777 Cov.: 31 AF XY: 0.370 AC XY: 27509 AN XY: 74266

African (AFR) AF: 0.296 AC: 12277 AN: 41440

American (AMR) AF: 0.315 AC: 4810 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1255 AN: 3472

East Asian (EAS) AF: 0.372 AC: 1918 AN: 5158

South Asian (SAS) AF: 0.432 AC: 2079 AN: 4818

European-Finnish (FIN) AF: 0.441 AC: 4656 AN: 10548

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28099 AN: 67956

Other (OTH) AF: 0.412 AC: 868 AN: 2108

Alfa AF: 0.398 Hom.: 45250

Bravo AF: 0.357

Asia WGS AF: 0.444 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	15
DANN	Benign	0.90
PhyloP100		0.73

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: rs6941421;

hg19: chr6-15089151;