rs1294410

Variant names:

• chr6-6738519-T-C
• rs1294410
• ENST00000648205.2:n.122+390A>G

Variant summary

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

The ENST00000648205.2(ENSG00000226281):​n.122+390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,082 control chromosomes in the GnomAD database, including 32,045 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 0.64 (32045 hom., cov: 32)
• Consequence: ENSG00000226281 ENST00000648205.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 38 publications found

Genes affected

ENSG00000226281 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928004	NR_187687.1	n.486-26661A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226281	ENST00000648205.2	n.122+390A>G		intron_variant	Intron 1 of 3
ENSG00000226281	ENST00000656346.2	n.119+390A>G		intron_variant	Intron 1 of 3
ENSG00000226281	ENST00000669831.2	n.189+390A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96904 AN: 151962 Hom.: 32026 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.638 AC: 96957 AN: 152082 Hom.: 32045 Cov.: 32 AF XY: 0.627 AC XY: 46632 AN XY: 74316

African (AFR) AF: 0.778 AC: 32261 AN: 41478

American (AMR) AF: 0.526 AC: 8045 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2183 AN: 3472

East Asian (EAS) AF: 0.227 AC: 1175 AN: 5174

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4814

European-Finnish (FIN) AF: 0.634 AC: 6712 AN: 10580

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.627 AC: 42619 AN: 67962

Other (OTH) AF: 0.594 AC: 1255 AN: 2112

Alfa AF: 0.627 Hom.: 106258

Bravo AF: 0.634

Asia WGS AF: 0.331 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.62
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1294410; hg19: chr6-6738752;