chr1-101284418-A-G

Variant names:

• chr1-101284418-A-G
• rs910633

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 0.506 in 152,058 control chromosomes in the GnomAD database, including 19,761 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 0.51 (19761 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 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: 0.506 AC: 76838 AN: 151940 Hom.: 19736 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.506 AC: 76893 AN: 152058 Hom.: 19761 Cov.: 33 AF XY: 0.500 AC XY: 37178 AN XY: 74348

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.507

Alfa AF: 0.499 Hom.: 33233

Bravo AF: 0.505

Asia WGS AF: 0.529 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs910633; hg19: chr1-101749974;