1-101414449-T-C

Variant names:

• chr1-101414449-T-C
• rs2338971

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 0.786 in 152,050 control chromosomes in the GnomAD database, including 47,289 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 0.79 (47289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.786 AC: 119415 AN: 151930 Hom.: 47248 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.786 AC: 119506 AN: 152050 Hom.: 47289 Cov.: 32 AF XY: 0.783 AC XY: 58210 AN XY: 74314

African (AFR) AF: 0.829 AC: 34396 AN: 41512

American (AMR) AF: 0.646 AC: 9852 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2742 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4190 AN: 5180

South Asian (SAS) AF: 0.718 AC: 3458 AN: 4818

European-Finnish (FIN) AF: 0.780 AC: 8259 AN: 10592

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53884 AN: 67908

Other (OTH) AF: 0.800 AC: 1689 AN: 2110

Alfa AF: 0.777 Hom.: 5383

Bravo AF: 0.774

Asia WGS AF: 0.765 AC: 2660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.38
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs2338971; hg19: chr1-101880005;