rs4310401

Variant names:

• chr1-80190429-A-G
• rs4310401

Your query was ambiguous. Multiple possible variants found:

• chr1-80190429-A-G
• chr1-80190429-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.344 in 151,964 control chromosomes in the GnomAD database, including 9,233 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 (9233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 52223 AN: 151848 Hom.: 9235 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.344 AC: 52229 AN: 151964 Hom.: 9233 Cov.: 32 AF XY: 0.343 AC XY: 25465 AN XY: 74282

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.352

Alfa AF: 0.376 Hom.: 22223

Bravo AF: 0.334

Asia WGS AF: 0.196 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4310401; hg19: chr1-80656114;