7-106702745-A-G

Variant names:

• chr7-106702745-A-G
• rs342247
• ENST00000490856.5:n.108+29597T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000490856.5(ENSG00000243797):​n.108+29597T>C 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 151,232 control chromosomes in the GnomAD database, including 9,867 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 (9867 hom., cov: 31)
• Consequence: ENSG00000243797 ENST00000490856.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 2 publications found

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490856.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243797	ENST00000490856.5	TSL:4	n.108+29597T>C		intron	N/A
	ENSG00000243797	ENST00000592441.1	TSL:2	n.172+57821T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52452 AN: 151116 Hom.: 9869 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.347 AC: 52462 AN: 151232 Hom.: 9867 Cov.: 31 AF XY: 0.347 AC XY: 25627 AN XY: 73884

African (AFR) AF: 0.201 AC: 8304 AN: 41226

American (AMR) AF: 0.329 AC: 5014 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1443 AN: 3458

East Asian (EAS) AF: 0.235 AC: 1204 AN: 5132

South Asian (SAS) AF: 0.340 AC: 1633 AN: 4800

European-Finnish (FIN) AF: 0.445 AC: 4621 AN: 10388

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29221 AN: 67710

Other (OTH) AF: 0.337 AC: 706 AN: 2098

Alfa AF: 0.326 Hom.: 2508

Bravo AF: 0.329

Asia WGS AF: 0.290 AC: 1005 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.39
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs342247; hg19: chr7-106343191;