rs10737578

Variant names:

• chr1-190014590-T-C
• rs10737578

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 0.717 in 151,902 control chromosomes in the GnomAD database, including 40,275 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 0.72 (40275 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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: 0.717 AC: 108842 AN: 151784 Hom.: 40197 Cov.: 31

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.717 AC: 108986 AN: 151902 Hom.: 40275 Cov.: 31 AF XY: 0.716 AC XY: 53118 AN XY: 74204

African (AFR) AF: 0.911 AC: 37767 AN: 41472

American (AMR) AF: 0.654 AC: 9958 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2295 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2593 AN: 5132

South Asian (SAS) AF: 0.661 AC: 3181 AN: 4810

European-Finnish (FIN) AF: 0.708 AC: 7475 AN: 10558

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43403 AN: 67934

Other (OTH) AF: 0.692 AC: 1456 AN: 2104

Alfa AF: 0.667 Hom.: 90603

Bravo AF: 0.720

Asia WGS AF: 0.639 AC: 2223 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	0.77
DANN	Benign	0.50
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10737578; hg19: chr1-189983720;