7-148560956-G-C

Variant names:

• chr7-148560956-G-C
• rs7807268
• ENST00000637240.2:n.346+1309C>G

Variant summary

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

The ENST00000637240.2(ENSG00000287636):​n.346+1309C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,702 control chromosomes in the GnomAD database, including 19,940 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 0.51 (19940 hom., cov: 30)
• Consequence: ENSG00000287636 ENST00000637240.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 19 publications found

Genes affected

ENSG00000287636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637240.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287636	ENST00000637240.2	TSL:5	n.346+1309C>G		intron	N/A
	ENSG00000287636	ENST00000715352.1		n.298+7144C>G		intron	N/A
	ENSG00000287636	ENST00000715353.1		n.841+7144C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77658 AN: 151590 Hom.: 19928 Cov.: 30

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.512 AC: 77717 AN: 151702 Hom.: 19940 Cov.: 30 AF XY: 0.513 AC XY: 38034 AN XY: 74150

African (AFR) AF: 0.474 AC: 19586 AN: 41354

American (AMR) AF: 0.547 AC: 8353 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2077 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1860 AN: 5144

South Asian (SAS) AF: 0.503 AC: 2408 AN: 4792

European-Finnish (FIN) AF: 0.482 AC: 5057 AN: 10500

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36578 AN: 67880

Other (OTH) AF: 0.538 AC: 1133 AN: 2104

Alfa AF: 0.383 Hom.: 1024

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.68
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7807268; hg19: chr7-148258048;