rs34175640

Variant names:

• chr1-11892155-T-C
• rs34175640

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 0.43 in 152,006 control chromosomes in the GnomAD database, including 14,506 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 0.43 (14506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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: 0.429 AC: 65212 AN: 151888 Hom.: 14480 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.430 AC: 65301 AN: 152006 Hom.: 14506 Cov.: 32 AF XY: 0.435 AC XY: 32327 AN XY: 74298

African (AFR) AF: 0.504 AC: 20890 AN: 41450

American (AMR) AF: 0.383 AC: 5852 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2672 AN: 5164

South Asian (SAS) AF: 0.463 AC: 2237 AN: 4828

European-Finnish (FIN) AF: 0.535 AC: 5651 AN: 10558

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25805 AN: 67948

Other (OTH) AF: 0.414 AC: 874 AN: 2110

Alfa AF: 0.417 Hom.: 2311

Bravo AF: 0.418

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.040
DANN	Benign	0.48
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs34175640; hg19: chr1-11952212;