6-14030239-C-A

Variant names:

• chr6-14030239-C-A
• rs1023107

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.155 AC: 6440 AN: 41498

American (AMR) AF: 0.302 AC: 4622 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1300 AN: 3466

East Asian (EAS) AF: 0.348 AC: 1799 AN: 5166

South Asian (SAS) AF: 0.306 AC: 1473 AN: 4810

European-Finnish (FIN) AF: 0.363 AC: 3839 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22610 AN: 67954

Other (OTH) AF: 0.301 AC: 637 AN: 2114

Alfa AF: 0.318 Hom.: 34058

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
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs1023107; hg19: chr6-14030470;