rs1441835

Positions:

• chr1-29699788-C-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 0.144 in 152,118 control chromosomes in the GnomAD database, including 3,305 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 0.14 (3305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21855 AN: 152000 Hom.: 3288 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.144 AC: 21911 AN: 152118 Hom.: 3305 Cov.: 32 AF XY: 0.144 AC XY: 10682 AN XY: 74348

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.00894

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0856

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.102

Alfa AF: 0.101 Hom.: 244

Bravo AF: 0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1441835; hg19: chr1-30172635;