chr1-34864921-A-C

Variant names:

• chr1-34864921-A-C
• rs11583978

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 0.343 in 151,164 control chromosomes in the GnomAD database, including 9,474 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 0.34 (9474 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 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: 0.344 AC: 51943 AN: 151050 Hom.: 9479 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.0311

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.343 AC: 51920 AN: 151164 Hom.: 9474 Cov.: 31 AF XY: 0.332 AC XY: 24486 AN XY: 73864

African (AFR) AF: 0.263 AC: 10825 AN: 41144

American (AMR) AF: 0.328 AC: 4987 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1277 AN: 3452

East Asian (EAS) AF: 0.0308 AC: 159 AN: 5158

South Asian (SAS) AF: 0.235 AC: 1124 AN: 4790

European-Finnish (FIN) AF: 0.308 AC: 3211 AN: 10416

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 28983 AN: 67688

Other (OTH) AF: 0.354 AC: 744 AN: 2102

Alfa AF: 0.263 Hom.: 818

Bravo AF: 0.346

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs11583978; hg19: chr1-35330522; COSMIC: COSV52398209;