rs4461829

Variant names:

• chr7-104229579-A-G
• rs4461829

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 0.292 in 152,008 control chromosomes in the GnomAD database, including 7,044 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 0.29 (7044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.292 AC: 44351 AN: 151890 Hom.: 7039 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.292 AC: 44380 AN: 152008 Hom.: 7044 Cov.: 32 AF XY: 0.300 AC XY: 22273 AN XY: 74298

African (AFR) AF: 0.275 AC: 11416 AN: 41446

American (AMR) AF: 0.442 AC: 6751 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2702 AN: 5166

South Asian (SAS) AF: 0.333 AC: 1599 AN: 4808

European-Finnish (FIN) AF: 0.294 AC: 3102 AN: 10562

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17048 AN: 67972

Other (OTH) AF: 0.294 AC: 621 AN: 2110

Alfa AF: 0.288 Hom.: 1849

Bravo AF: 0.302

Asia WGS AF: 0.390 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.63
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4461829; hg19: chr7-103870027;