1-238136541-C-A

Position:

• chr1-238136541-C-A

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 0.0463 in 152,304 control chromosomes in the GnomAD database, including 193 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 0.046 (193 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.238136541C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7044 AN: 152186 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0526

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0314

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.0356

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0463 AC: 7052 AN: 152304 Hom.: 193 Cov.: 32 AF XY: 0.0458 AC XY: 3412 AN XY: 74478

Gnomad4 AFR AF: 0.0529

Gnomad4 AMR AF: 0.0313

Gnomad4 ASJ AF: 0.0891

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0436 Hom.: 234

Bravo AF: 0.0446

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.90
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16836417; hg19: chr1-238299841; COSMIC: COSV60041963;