6-10371418-A-G

Variant names:

• chr6-10371418-A-G
• rs12663250
• ENST00000784772.1:n.244-3299T>C

Variant summary

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

The ENST00000784772.1(ENSG00000302171):​n.244-3299T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 152,218 control chromosomes in the GnomAD database, including 583 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 0.047 (583 hom., cov: 33)
• Consequence: ENSG00000302171 ENST00000784772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789
• Publications: 2 publications found

Genes affected

ENSG00000302171 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 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
ENSG00000302171	ENST00000784772.1	n.244-3299T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7173 AN: 152102 Hom.: 583 Cov.: 33

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0501

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

GnomAD4 genome AF: 0.0472 AC: 7178 AN: 152218 Hom.: 583 Cov.: 33 AF XY: 0.0506 AC XY: 3764 AN XY: 74422

African (AFR) AF: 0.0181 AC: 753 AN: 41546

American (AMR) AF: 0.0837 AC: 1278 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2181 AN: 5188

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4826

European-Finnish (FIN) AF: 0.0368 AC: 389 AN: 10576

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0309 AC: 2099 AN: 68022

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0574 Hom.: 250

Bravo AF: 0.0546

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.50
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs12663250; hg19: chr6-10371651;