rs1110701

Positions:

• chr7-50410929-A-G
• chr7-50410929-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.281

Alfa AF: 0.158 Hom.: 317

Bravo AF: 0.275

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1110701; hg19: chr7-50478627;