6-104465169-A-G

Variant summary

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

The XR_001744272.2(LOC105377918):n.1208-2046T>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 0.797 in 152,146 control chromosomes in the GnomAD database, including 48,723 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 0.80 (48723 hom., cov: 33)
• Consequence: LOC105377918 XR_001744272.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

LOC105377918 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377918	XR_001744272.2	n.1208-2046T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121124 AN: 152028 Hom.: 48674 Cov.: 33

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.797 AC: 121234 AN: 152146 Hom.: 48723 Cov.: 33 AF XY: 0.800 AC XY: 59525 AN XY: 74378

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.847

Alfa AF: 0.837 Hom.: 55324

Bravo AF: 0.798

Asia WGS AF: 0.819 AC: 2843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.3
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs408949; hg19: chr6-104913044;