rs1403155

Variant names:

• chr7-68585426-G-A
• rs1403155

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 0.0309 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.00643 AC: 267 AN: 41528

American (AMR) AF: 0.0661 AC: 1009 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3470

East Asian (EAS) AF: 0.166 AC: 858 AN: 5166

South Asian (SAS) AF: 0.0357 AC: 172 AN: 4820

European-Finnish (FIN) AF: 0.0983 AC: 1038 AN: 10564

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0177 AC: 1203 AN: 68006

Other (OTH) AF: 0.0241 AC: 51 AN: 2112

Alfa AF: 0.0251 Hom.: 294

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1403155; hg19: chr7-68050413;