rs12744671

Positions:

• chr1-68466239-A-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 0.0658 in 152,212 control chromosomes in the GnomAD database, including 444 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 0.066 (444 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

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 (NFE) allele frequency at 95% confidence interval = 0.0996 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: 0.0659 AC: 10022 AN: 152094 Hom.: 445 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0658 AC: 10017 AN: 152212 Hom.: 444 Cov.: 32 AF XY: 0.0632 AC XY: 4706 AN XY: 74436

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0665

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0613

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0890 Hom.: 371

Bravo AF: 0.0645

Asia WGS AF: 0.0150 AC: 52 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	2.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12744671; hg19: chr1-68931922;