rs1441835

Variant names:

• chr1-29699788-C-G
• rs1441835

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;