rs342286

Positions:

• chr7-106724153-A-G

Variant summary

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

The ENST00000490856.5(ENSG00000243797):​n.108+8189T>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 0.333 in 152,042 control chromosomes in the GnomAD database, including 9,985 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 0.33 (9985 hom., cov: 31)
• Consequence: ENST00000490856.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 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
	ENST00000490856.5	n.108+8189T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000592441.1	n.172+36413T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50602 AN: 151924 Hom.: 9982 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.333 AC: 50608 AN: 152042 Hom.: 9985 Cov.: 31 AF XY: 0.334 AC XY: 24799 AN XY: 74298

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.333

Alfa AF: 0.377 Hom.: 1646

Bravo AF: 0.312

Asia WGS AF: 0.308 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342286; hg19: chr7-106364599;