chr6-91366220-T-C

Variant names:

• chr6-91366220-T-C
• rs6454855
• XR_001744260.1:n.335-429T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001744260.1(LOC107986624):​n.335-429T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,018 control chromosomes in the GnomAD database, including 25,631 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 0.57 (25631 hom., cov: 32)
• Consequence: LOC107986624 XR_001744260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 2 publications found

Genes affected

LOC107986624 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86438 AN: 151900 Hom.: 25587 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.569 AC: 86540 AN: 152018 Hom.: 25631 Cov.: 32 AF XY: 0.573 AC XY: 42535 AN XY: 74274

African (AFR) AF: 0.718 AC: 29797 AN: 41492

American (AMR) AF: 0.597 AC: 9113 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2020 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3734 AN: 5138

South Asian (SAS) AF: 0.566 AC: 2731 AN: 4826

European-Finnish (FIN) AF: 0.505 AC: 5333 AN: 10564

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32087 AN: 67954

Other (OTH) AF: 0.550 AC: 1160 AN: 2108

Alfa AF: 0.409 Hom.: 1198

Bravo AF: 0.585

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.49
DANN	Benign	0.58
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs6454855; hg19: chr6-92075938; COSMIC: COSV60245079;