rs7750009

Variant names:

• chr6-14006007-A-G
• rs7750009
• ENST00000427011.1:n.62-570A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000427011.1(ENSG00000233981):​n.62-570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,784 control chromosomes in the GnomAD database, including 9,492 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 0.35 (9492 hom., cov: 31)
• Consequence: ENSG00000233981 ENST00000427011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

Genes affected

ENSG00000233981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 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
ENSG00000233981	ENST00000427011.1	n.62-570A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52618 AN: 151670 Hom.: 9486 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.347 AC: 52644 AN: 151784 Hom.: 9492 Cov.: 31 AF XY: 0.347 AC XY: 25758 AN XY: 74138

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.379

Alfa AF: 0.373 Hom.: 4950

Bravo AF: 0.338

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	14
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7750009; hg19: chr6-14006238;