chr6-119923639-G-A

Position:

• chr6-119923639-G-A

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 0.163 in 152,184 control chromosomes in the GnomAD database, including 2,208 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 0.16 (2208 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.163 AC: 24764 AN: 152066 Hom.: 2208 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.163 AC: 24771 AN: 152184 Hom.: 2208 Cov.: 32 AF XY: 0.160 AC XY: 11895 AN XY: 74408

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.164

Alfa AF: 0.164 Hom.: 4450

Bravo AF: 0.162

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484965; hg19: chr6-120244785; COSMIC: COSV69423040;