7-48765243-A-G

Variant names:

• chr7-48765243-A-G
• rs10487572

Variant summary

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

The variant allele was found at a frequency of 0.426 in 151,994 control chromosomes in the GnomAD database, including 14,038 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 0.43 (14038 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64719 AN: 151874 Hom.: 14038 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.426 AC: 64735 AN: 151994 Hom.: 14038 Cov.: 32 AF XY: 0.432 AC XY: 32091 AN XY: 74310

African (AFR) AF: 0.363 AC: 15031 AN: 41454

American (AMR) AF: 0.421 AC: 6422 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3066 AN: 5156

South Asian (SAS) AF: 0.464 AC: 2235 AN: 4814

European-Finnish (FIN) AF: 0.479 AC: 5063 AN: 10576

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30088 AN: 67934

Other (OTH) AF: 0.428 AC: 905 AN: 2116

Alfa AF: 0.439 Hom.: 7683

Bravo AF: 0.416

Asia WGS AF: 0.470 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.58
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs10487572; hg19: chr7-48804839;