chr6-121810339-T-C

Position:

• chr6-121810339-T-C

Variant summary

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

The XR_942936.3(LOC105377979):​n.237+42724T>C 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 152,032 control chromosomes in the GnomAD database, including 6,510 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 (6510 hom., cov: 32)
• Consequence: LOC105377979 XR_942936.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

Genes affected

LOC105377979 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377979	XR_942936.3	n.237+42724T>C		intron_variant, non_coding_transcript_variant
LOC105377979	XR_942937.4	n.237+42724T>C		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: 34522 AN: 151914 Hom.: 6477 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0981

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0997

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: 34602 AN: 152032 Hom.: 6510 Cov.: 32 AF XY: 0.226 AC XY: 16828 AN XY: 74322

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0981

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0997

Gnomad4 OTH AF: 0.202

Alfa AF: 0.206 Hom.: 839

Bravo AF: 0.241

Asia WGS AF: 0.301 AC: 1043 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015451; hg19: chr6-122131485;