rs697763

Positions:

• chr1-228004921-G-C

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 0.739 in 152,116 control chromosomes in the GnomAD database, including 42,383 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 0.74 (42383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

ACMG classification

Verdict is Benign. Variant got -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 = 0.884 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112273 AN: 151998 Hom.: 42326 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.739 AC: 112387 AN: 152116 Hom.: 42383 Cov.: 32 AF XY: 0.746 AC XY: 55493 AN XY: 74338

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.717

Alfa AF: 0.698 Hom.: 4645

Bravo AF: 0.740

Asia WGS AF: 0.879 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs697763; hg19: chr1-228192622; COSMIC: COSV52729760;