rs854549

Variant names:

• chr7-95297273-C-A
• rs854549

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 0.26 in 152,136 control chromosomes in the GnomAD database, including 5,902 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 0.26 (5902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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: 0.260 AC: 39507 AN: 152016 Hom.: 5901 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.260 AC: 39512 AN: 152136 Hom.: 5902 Cov.: 32 AF XY: 0.254 AC XY: 18918 AN XY: 74358

African (AFR) AF: 0.141 AC: 5845 AN: 41512

American (AMR) AF: 0.252 AC: 3856 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1415 AN: 3472

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5178

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4818

European-Finnish (FIN) AF: 0.276 AC: 2912 AN: 10566

Middle Eastern (MID) AF: 0.469 AC: 136 AN: 290

European-Non Finnish (NFE) AF: 0.341 AC: 23161 AN: 67992

Other (OTH) AF: 0.298 AC: 630 AN: 2116

Alfa AF: 0.319 Hom.: 10353

Bravo AF: 0.253

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.69
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs854549; hg19: chr7-94926585;