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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929770	XR_007059596.1	n.251+3247T>C		intron_variant	Intron 1 of 2
LOC101929770	XR_007059597.1	n.251+3247T>C		intron_variant	Intron 1 of 1
LOC101929770	XR_007059598.1	n.144+6536T>C		intron_variant	Intron 1 of 1
LOC101929770	XR_926855.3	n.144+6536T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286417	ENST00000671451.2	n.195+6536T>C		intron_variant	Intron 1 of 2
ENSG00000286417	ENST00000811306.1	n.173+6536T>C		intron_variant	Intron 1 of 3
ENSG00000286417	ENST00000811307.1	n.187+6536T>C		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs227855; hg19: chr6-44702352;