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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.300 AC: 12444 AN: 41432

American (AMR) AF: 0.317 AC: 4840 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1353 AN: 3468

East Asian (EAS) AF: 0.186 AC: 958 AN: 5160

South Asian (SAS) AF: 0.265 AC: 1277 AN: 4818

European-Finnish (FIN) AF: 0.423 AC: 4455 AN: 10540

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.380 AC: 25845 AN: 67950

Other (OTH) AF: 0.352 AC: 743 AN: 2110

Alfa AF: 0.368 Hom.: 45143

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4310401; hg19: chr1-80656114;