rs1074073

Variant names:

• chr1-29814163-T-A
• rs1074073

Your query was ambiguous. Multiple possible variants found:

• chr1-29814163-T-A
• chr1-29814163-T-G

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 0.364 in 151,922 control chromosomes in the GnomAD database, including 10,478 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 0.36 (10478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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: 0.364 AC: 55237 AN: 151804 Hom.: 10473 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.364 AC: 55278 AN: 151922 Hom.: 10478 Cov.: 32 AF XY: 0.361 AC XY: 26771 AN XY: 74246

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.390

Alfa AF: 0.383 Hom.: 1413

Bravo AF: 0.362

Asia WGS AF: 0.276 AC: 961 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074073; hg19: chr1-30287010;