rs7812975

Positions:

• chr8-25597766-G-A
• chr8-25597766-G-T

Variant summary

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

The ENST00000670669.1(ENSG00000253100):​n.130+4440G>A 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 0.606 in 152,030 control chromosomes in the GnomAD database, including 29,717 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 0.61 (29717 hom., cov: 32)
• Consequence: ENST00000670669.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670669.1	n.130+4440G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92110 AN: 151912 Hom.: 29712 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.606 AC: 92123 AN: 152030 Hom.: 29717 Cov.: 32 AF XY: 0.608 AC XY: 45139 AN XY: 74282

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.625

Alfa AF: 0.677 Hom.: 17704

Bravo AF: 0.603

Asia WGS AF: 0.736 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.24
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7812975; hg19: chr8-25455282;