chr7-46631145-A-G

Position:

• chr7-46631145-A-G

Variant summary

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

The variant allele was found at a frequency of 0.458 in 151,912 control chromosomes in the GnomAD database, including 16,477 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 0.46 (16477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69484 AN: 151794 Hom.: 16475 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.458 AC: 69505 AN: 151912 Hom.: 16477 Cov.: 32 AF XY: 0.452 AC XY: 33594 AN XY: 74244

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.504

Alfa AF: 0.500 Hom.: 37934

Bravo AF: 0.473

Asia WGS AF: 0.359 AC: 1241 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs993183; hg19: chr7-46670743;