rs806276

Variant names:

• chr6-90497632-A-G
• rs806276
• XR_007059678.1:n.3208+441T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-90497632-A-G
• chr6-90497632-A-T

Variant summary

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

The XR_007059678.1(LOC124901362):​n.3208+441T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,964 control chromosomes in the GnomAD database, including 14,695 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 0.42 (14695 hom., cov: 32)
• Consequence: LOC124901362 XR_007059678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 15 publications found

Genes affected

LOC124901362 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 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: 0.419 AC: 63625 AN: 151846 Hom.: 14669 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.419 AC: 63702 AN: 151964 Hom.: 14695 Cov.: 32 AF XY: 0.414 AC XY: 30764 AN XY: 74286

African (AFR) AF: 0.630 AC: 26071 AN: 41398

American (AMR) AF: 0.367 AC: 5608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1593 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1313 AN: 5170

South Asian (SAS) AF: 0.263 AC: 1264 AN: 4810

European-Finnish (FIN) AF: 0.306 AC: 3237 AN: 10574

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23325 AN: 67944

Other (OTH) AF: 0.407 AC: 860 AN: 2112

Alfa AF: 0.368 Hom.: 43995

Bravo AF: 0.434

Asia WGS AF: 0.335 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.8
DANN	Benign	0.46
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs806276; hg19: chr6-91207351; COSMIC: COSV60243799;