rs2191265

chr7-12865442-A-G

Variant summary

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

The ENST00000639998.1(ENSG00000229618):n.483+107126A>G 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 0.543 in 151,904 control chromosomes in the GnomAD database, including 23,539 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 0.54 (23539 hom., cov: 31)
• Consequence: ENST00000639998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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
	ENST00000639998.1	n.483+107126A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000638964.1	n.484+62710A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82367 AN: 151786 Hom.: 23518 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.543 AC: 82421 AN: 151904 Hom.: 23539 Cov.: 31 AF XY: 0.543 AC XY: 40313 AN XY: 74238

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.541

Alfa AF: 0.504 Hom.: 3394

Bravo AF: 0.548

Asia WGS AF: 0.530 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2191265; hg19: chr7-12905067;