rs227855

Variant names:

• chr6-44734615-T-C
• rs227855
• ENST00000671451.2:n.195+6536T>C

Variant summary

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

The ENST00000671451.2(ENSG00000286417):​n.195+6536T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,100 control chromosomes in the GnomAD database, including 34,719 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 0.66 (34719 hom., cov: 32)
• Consequence: ENSG00000286417 ENST00000671451.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 3 publications found

Genes affected

ENSG00000286417 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671451.2. 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
	ENSG00000286417	ENST00000671451.2		n.195+6536T>C		intron	N/A
	ENSG00000286417	ENST00000811306.1		n.173+6536T>C		intron	N/A
	ENSG00000286417	ENST00000811307.1		n.187+6536T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100986 AN: 151982 Hom.: 34672 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.665 AC: 101081 AN: 152100 Hom.: 34719 Cov.: 32 AF XY: 0.664 AC XY: 49360 AN XY: 74348

African (AFR) AF: 0.847 AC: 35171 AN: 41520

American (AMR) AF: 0.669 AC: 10214 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2183 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2280 AN: 5156

South Asian (SAS) AF: 0.605 AC: 2919 AN: 4822

European-Finnish (FIN) AF: 0.594 AC: 6268 AN: 10560

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40013 AN: 67984

Other (OTH) AF: 0.643 AC: 1359 AN: 2112

Alfa AF: 0.633 Hom.: 3876

Bravo AF: 0.681

Asia WGS AF: 0.535 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.38
PhyloP100		-0.40

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: rs227855;

hg19: chr6-44702352;