chr7-50410929-A-G

Variant names:

• chr7-50410929-A-G
• rs1110701

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 0.28 in 152,016 control chromosomes in the GnomAD database, including 6,124 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 0.28 (6124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42554 AN: 151896 Hom.: 6111 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.280 AC: 42605 AN: 152016 Hom.: 6124 Cov.: 32 AF XY: 0.284 AC XY: 21071 AN XY: 74312

African (AFR) AF: 0.280 AC: 11607 AN: 41456

American (AMR) AF: 0.258 AC: 3943 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.105 AC: 542 AN: 5154

South Asian (SAS) AF: 0.301 AC: 1449 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3561 AN: 10572

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19707 AN: 67946

Other (OTH) AF: 0.281 AC: 593 AN: 2112

Alfa AF: 0.271 Hom.: 7739

Bravo AF: 0.275

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.020
DANN	Benign	0.19
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs1110701; hg19: chr7-50478627;