7-148561069-C-T

Position:

• chr7-148561069-C-T

Variant summary

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

The ENST00000637240.1(ENSG00000283648):​n.346+1196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,136 control chromosomes in the GnomAD database, including 5,473 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 0.26 (5473 hom., cov: 30)
• Consequence: ENSG00000283648 ENST00000637240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

Genes affected

ENSG00000283648 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901766	XR_007060577.1	n.269+7031G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000283648	ENST00000637240.1	n.346+1196G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39505 AN: 151020 Hom.: 5469 Cov.: 30

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.262 AC: 39543 AN: 151136 Hom.: 5473 Cov.: 30 AF XY: 0.261 AC XY: 19281 AN XY: 73782

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.265

Alfa AF: 0.293 Hom.: 11247

Bravo AF: 0.264

Asia WGS AF: 0.221 AC: 765 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12704036; hg19: chr7-148258161;