1-237933739-C-G

Variant names:

• chr1-237933739-C-G
• rs540782

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 0.609 in 151,968 control chromosomes in the GnomAD database, including 28,397 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 0.61 (28397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 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: 0.609 AC: 92473 AN: 151850 Hom.: 28372 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.609 AC: 92546 AN: 151968 Hom.: 28397 Cov.: 32 AF XY: 0.610 AC XY: 45342 AN XY: 74284

African (AFR) AF: 0.693 AC: 28725 AN: 41434

American (AMR) AF: 0.565 AC: 8634 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2187 AN: 3466

East Asian (EAS) AF: 0.514 AC: 2648 AN: 5152

South Asian (SAS) AF: 0.599 AC: 2884 AN: 4812

European-Finnish (FIN) AF: 0.595 AC: 6276 AN: 10548

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39181 AN: 67956

Other (OTH) AF: 0.606 AC: 1282 AN: 2116

Alfa AF: 0.446 Hom.: 1110

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs540782; hg19: chr1-238097039;