chr6-90795693-C-T

Position:

• chr6-90795693-C-T

Variant summary

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

The XR_001744259.1(LOC107986623):​n.1244-112363C>T 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 0.398 in 151,906 control chromosomes in the GnomAD database, including 12,151 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 0.40 (12151 hom., cov: 32)
• Consequence: LOC107986623 XR_001744259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

LOC107986623 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986623	XR_001744259.1	n.1244-112363C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60388 AN: 151788 Hom.: 12137 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.398 AC: 60454 AN: 151906 Hom.: 12151 Cov.: 32 AF XY: 0.406 AC XY: 30127 AN XY: 74232

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.385

Alfa AF: 0.352 Hom.: 19631

Bravo AF: 0.395

Asia WGS AF: 0.478 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485409; hg19: chr6-91505411;