rs854572

Variant names:

• chr7-95325384-C-G
• rs854572

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 0.41 in 152,048 control chromosomes in the GnomAD database, including 14,889 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 0.41 (14889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 62 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 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: 0.410 AC: 62298 AN: 151930 Hom.: 14893 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.410 AC: 62305 AN: 152048 Hom.: 14889 Cov.: 32 AF XY: 0.407 AC XY: 30237 AN XY: 74314

African (AFR) AF: 0.156 AC: 6477 AN: 41496

American (AMR) AF: 0.507 AC: 7745 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2189 AN: 3464

East Asian (EAS) AF: 0.445 AC: 2292 AN: 5146

South Asian (SAS) AF: 0.413 AC: 1992 AN: 4818

European-Finnish (FIN) AF: 0.374 AC: 3950 AN: 10566

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36059 AN: 67958

Other (OTH) AF: 0.485 AC: 1025 AN: 2112

Alfa AF: 0.447 Hom.: 2072

Bravo AF: 0.412

Asia WGS AF: 0.404 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs854572; hg19: chr7-94954696;