rs1414411

Variant names:

• chr1-80072504-T-C
• rs1414411

Your query was ambiguous. Multiple possible variants found:

• chr1-80072504-T-C
• chr1-80072504-T-G

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 0.305 in 152,042 control chromosomes in the GnomAD database, including 9,169 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 0.30 (9169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 4 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 = 0.553 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: 0.304 AC: 46245 AN: 151926 Hom.: 9147 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.305 AC: 46318 AN: 152042 Hom.: 9169 Cov.: 32 AF XY: 0.305 AC XY: 22685 AN XY: 74326

African (AFR) AF: 0.559 AC: 23178 AN: 41454

American (AMR) AF: 0.229 AC: 3506 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3472

East Asian (EAS) AF: 0.390 AC: 2006 AN: 5150

South Asian (SAS) AF: 0.423 AC: 2037 AN: 4820

European-Finnish (FIN) AF: 0.153 AC: 1623 AN: 10588

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.179 AC: 12155 AN: 67964

Other (OTH) AF: 0.295 AC: 621 AN: 2108

Alfa AF: 0.231 Hom.: 3011

Bravo AF: 0.321

Asia WGS AF: 0.401 AC: 1395 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	3.4
DANN	Benign	0.47
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs1414411; hg19: chr1-80538189;