7-148560956-G-C

Variant names:

• chr7-148560956-G-C
• rs7807268
• ENST00000637240.1:n.346+1309C>G

Variant summary

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

The ENST00000637240.1(ENSG00000283648):​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: ENSG00000283648 ENST00000637240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

ENSG00000283648 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901766	XR_007060577.1	n.269+7144C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283648	ENST00000637240.1	n.346+1309C>G		intron_variant	Intron 4 of 5	5

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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.538

Alfa AF: 0.383 Hom.: 1024

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7807268; hg19: chr7-148258048;