rs853964

chr6-126708122-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000651326.1(ENSG00000293110):n.694-104657C>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 0.0226 in 152,152 control chromosomes in the GnomAD database, including 53 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 0.023 (53 hom., cov: 32)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0226 (3443/152152) while in subpopulation NFE AF= 0.0295 (2008/67996). AF 95% confidence interval is 0.0285. There are 53 homozygotes in gnomad4. There are 1792 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 53 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377992	XR_001743836.2	n.1069+1756G>A		intron_variant, non_coding_transcript_variant
LOC105377993	XR_001743837.2	n.79-6016C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651326.1	n.694-104657C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0227 AC: 3447 AN: 152034 Hom.: 53 Cov.: 32

Gnomad AFR AF: 0.00584

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.0634

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0296

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0226 AC: 3443 AN: 152152 Hom.: 53 Cov.: 32 AF XY: 0.0241 AC XY: 1792 AN XY: 74362

Gnomad4 AFR AF: 0.00582

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00352

Gnomad4 FIN AF: 0.0634

Gnomad4 NFE AF: 0.0295

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0272 Hom.: 65

Bravo AF: 0.0186

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
Cadd	Benign	18
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853964; hg19: chr6-127029267;