rs1607504

Variant names:

• chr3-135875394-G-A
• rs1607504

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 0.218 in 151,972 control chromosomes in the GnomAD database, including 3,822 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 0.22 (3822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.218 AC: 33080 AN: 151854 Hom.: 3815 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.218 AC: 33108 AN: 151972 Hom.: 3822 Cov.: 32 AF XY: 0.218 AC XY: 16172 AN XY: 74274

African (AFR) AF: 0.276 AC: 11418 AN: 41402

American (AMR) AF: 0.147 AC: 2239 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3470

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5172

South Asian (SAS) AF: 0.156 AC: 753 AN: 4820

European-Finnish (FIN) AF: 0.279 AC: 2943 AN: 10552

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14412 AN: 67970

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.210 Hom.: 5586

Bravo AF: 0.210

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.58
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1607504; hg19: chr3-135594236;