rs607375

chr1-67688403-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 0.637 in 152,324 control chromosomes in the GnomAD database, including 31,544 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 0.64 (31489 hom., cov: 33)
  • Exomes 𝑓: 0.66 (55 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96737 AN: 151964 Hom.: 31467 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.658

GnomAD4 exome AF: 0.661 AC: 160 AN: 242 Hom.: 55 AF XY: 0.651 AC XY: 95 AN XY: 146

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.659

Gnomad4 NFE exome AF: 0.800

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.637 AC: 96804 AN: 152082 Hom.: 31489 Cov.: 33 AF XY: 0.634 AC XY: 47181 AN XY: 74360

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.660

Alfa AF: 0.671 Hom.: 4317

Bravo AF: 0.630

Asia WGS AF: 0.653 AC: 2269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs607375; hg19: chr1-68154086;