6-121824888-C-A

Position:

• chr6-121824888-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_942936.3(LOC105377979):​n.238-33023C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,880 control chromosomes in the GnomAD database, including 6,505 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 0.23 (6505 hom., cov: 32)
• Consequence: LOC105377979 XR_942936.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

LOC105377979 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377979	XR_942936.3	n.238-33023C>A		intron_variant, non_coding_transcript_variant
LOC105377979	XR_942937.4	n.237+57273C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34499 AN: 151760 Hom.: 6472 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.228 AC: 34580 AN: 151880 Hom.: 6505 Cov.: 32 AF XY: 0.226 AC XY: 16802 AN XY: 74224

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0976

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.0998

Gnomad4 OTH AF: 0.202

Alfa AF: 0.129 Hom.: 2299

Bravo AF: 0.241

Asia WGS AF: 0.304 AC: 1052 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9398652; hg19: chr6-122146034;