rs1403155

Positions:

• chr7-68585426-G-A

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 0.0309 in 152,146 control chromosomes in the GnomAD database, including 200 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 0.031 (200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0309 AC: 4700 AN: 152028 Hom.: 199 Cov.: 32

Gnomad AFR AF: 0.00645

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0983

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0309 AC: 4706 AN: 152146 Hom.: 200 Cov.: 32 AF XY: 0.0355 AC XY: 2638 AN XY: 74370

Gnomad4 AFR AF: 0.00643

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0357

Gnomad4 FIN AF: 0.0983

Gnomad4 NFE AF: 0.0177

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0270 Hom.: 92

Bravo AF: 0.0300

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.048
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1403155; hg19: chr7-68050413;