rs7077596

Positions:

• chr10-45017237-C-G

Variant summary

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

The ENST00000456938.6(ENSG00000293022):​n.412-1069G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,052 control chromosomes in the GnomAD database, including 20,676 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 0.49 (20676 hom., cov: 32)
• Consequence: ENST00000456938.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000456938.6	n.412-1069G>C		intron_variant, non_coding_transcript_variant		1
	ENST00000598522.5	n.765-1069G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74665 AN: 151934 Hom.: 20674 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.491 AC: 74671 AN: 152052 Hom.: 20676 Cov.: 32 AF XY: 0.494 AC XY: 36713 AN XY: 74322

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.510

Alfa AF: 0.545 Hom.: 3017

Bravo AF: 0.471

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7077596; hg19: chr10-45512685;