rs1464851

Variant names:

• chr7-70955026-G-A
• rs1464851

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 151,914 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.555 AC: 22990 AN: 41426

American (AMR) AF: 0.448 AC: 6840 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1772 AN: 5140

South Asian (SAS) AF: 0.408 AC: 1962 AN: 4812

European-Finnish (FIN) AF: 0.241 AC: 2544 AN: 10562

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25960 AN: 67936

Other (OTH) AF: 0.407 AC: 858 AN: 2110

Alfa AF: 0.401 Hom.: 1668

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1464851; hg19: chr7-70420012;