rs1023107

Positions:

• chr6-14030239-C-A
• chr6-14030239-C-G

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 0.283 in 152,060 control chromosomes in the GnomAD database, including 6,705 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 0.28 (6705 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 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: 0.283 AC: 43068 AN: 151942 Hom.: 6705 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.283 AC: 43072 AN: 152060 Hom.: 6705 Cov.: 31 AF XY: 0.284 AC XY: 21129 AN XY: 74336

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.301

Alfa AF: 0.323 Hom.: 16522

Bravo AF: 0.274

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023107; hg19: chr6-14030470;