rs227849

Variant names:

• chr6-44730971-G-A
• rs227849
• ENST00000671451.2:n.195+2892G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-44730971-G-A
• chr6-44730971-G-C

Variant summary

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

The ENST00000671451.2(ENSG00000286417):​n.195+2892G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,138 control chromosomes in the GnomAD database, including 25,746 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 0.58 (25746 hom., cov: 33)
• Consequence: ENSG00000286417 ENST00000671451.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80
• Publications: 13 publications found

Genes affected

ENSG00000286417 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929770	XR_007059598.1	n.144+2892G>A		intron_variant	Intron 1 of 1
LOC101929770	XR_926855.3	n.144+2892G>A		intron_variant	Intron 1 of 2
LOC101929770	XR_007059596.1	n.-147G>A		upstream_gene_variant
LOC101929770	XR_007059597.1	n.-147G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286417	ENST00000671451.2	n.195+2892G>A		intron_variant	Intron 1 of 2
ENSG00000286417	ENST00000811306.1	n.173+2892G>A		intron_variant	Intron 1 of 3
ENSG00000286417	ENST00000811307.1	n.187+2892G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.579 AC: 88011 AN: 152020 Hom.: 25710 Cov.: 33

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.579 AC: 88091 AN: 152138 Hom.: 25746 Cov.: 33 AF XY: 0.580 AC XY: 43131 AN XY: 74364

African (AFR) AF: 0.629 AC: 26117 AN: 41500

American (AMR) AF: 0.601 AC: 9200 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1966 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1608 AN: 5168

South Asian (SAS) AF: 0.508 AC: 2447 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6154 AN: 10572

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38834 AN: 67990

Other (OTH) AF: 0.561 AC: 1187 AN: 2114

Alfa AF: 0.565 Hom.: 8263

Bravo AF: 0.583

Asia WGS AF: 0.415 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs227849; hg19: chr6-44698708;