rs1464851

chr7-70955026-G-A

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 0.426 in 151,914 control chromosomes in the GnomAD database, including 14,358 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 (14358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 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: 0.426 AC: 64604 AN: 151796 Hom.: 14328 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.426 AC: 64692 AN: 151914 Hom.: 14358 Cov.: 32 AF XY: 0.422 AC XY: 31334 AN XY: 74266

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.407

Alfa AF: 0.395 Hom.: 1549

Bravo AF: 0.441

Asia WGS AF: 0.419 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.3
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1464851; hg19: chr7-70420012;