rs1670754

Variant names:

• chr4-32263375-G-A
• rs1670754

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 0.237 in 152,066 control chromosomes in the GnomAD database, including 4,668 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 0.24 (4668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.237 AC: 36070 AN: 151948 Hom.: 4657 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.237 AC: 36104 AN: 152066 Hom.: 4668 Cov.: 32 AF XY: 0.236 AC XY: 17530 AN XY: 74348

African (AFR) AF: 0.333 AC: 13795 AN: 41448

American (AMR) AF: 0.202 AC: 3082 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3470

East Asian (EAS) AF: 0.188 AC: 974 AN: 5170

South Asian (SAS) AF: 0.290 AC: 1399 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1505 AN: 10588

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14111 AN: 67974

Other (OTH) AF: 0.214 AC: 453 AN: 2112

Alfa AF: 0.217 Hom.: 16890

Bravo AF: 0.242

Asia WGS AF: 0.237 AC: 820 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.33
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1670754; hg19: chr4-32264997;