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. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000437648.1(ENSG00000234261):​n.228+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 ENST00000437648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733

Genes affected

ENSG00000234261 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234261	ENST00000437648.1	n.228+856A>G		intron_variant	Intron 1 of 3	5
ENSG00000234261	ENST00000653525.1	n.139+856A>G		intron_variant	Intron 1 of 3
ENSG00000234261	ENST00000656344.1	n.395+856A>G		intron_variant	Intron 1 of 4

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

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.412

Alfa AF: 0.404 Hom.: 28932

Bravo AF: 0.357

Asia WGS AF: 0.444 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6941421; hg19: chr6-15089151;