1-195945143-A-G

Variant names:

• chr1-195945143-A-G
• rs7517337

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 0.486 in 151,964 control chromosomes in the GnomAD database, including 18,629 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 0.49 (18629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 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: 0.486 AC: 73796 AN: 151846 Hom.: 18609 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.486 AC: 73870 AN: 151964 Hom.: 18629 Cov.: 32 AF XY: 0.492 AC XY: 36556 AN XY: 74276

African (AFR) AF: 0.548 AC: 22731 AN: 41444

American (AMR) AF: 0.523 AC: 7997 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1419 AN: 3466

East Asian (EAS) AF: 0.853 AC: 4415 AN: 5178

South Asian (SAS) AF: 0.489 AC: 2354 AN: 4812

European-Finnish (FIN) AF: 0.523 AC: 5514 AN: 10548

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27881 AN: 67924

Other (OTH) AF: 0.469 AC: 991 AN: 2112

Alfa AF: 0.442 Hom.: 73537

Bravo AF: 0.495

Asia WGS AF: 0.601 AC: 2092 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.74
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7517337; hg19: chr1-195914273;