chr6-37336610-A-G

Variant names:

• chr6-37336610-A-G
• rs195371
• XR_007059566.1:n.296-2205T>C

Variant summary

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

The XR_007059566.1(LOC105375040):​n.296-2205T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,624 control chromosomes in the GnomAD database, including 9,500 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 0.33 (9500 hom., cov: 32)
• Consequence: LOC105375040 XR_007059566.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

Genes affected

LOC105375040 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50244 AN: 151508 Hom.: 9481 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.332 AC: 50317 AN: 151624 Hom.: 9500 Cov.: 32 AF XY: 0.332 AC XY: 24604 AN XY: 74066

African (AFR) AF: 0.517 AC: 21371 AN: 41328

American (AMR) AF: 0.332 AC: 5052 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1028 AN: 3468

East Asian (EAS) AF: 0.120 AC: 618 AN: 5154

South Asian (SAS) AF: 0.204 AC: 979 AN: 4796

European-Finnish (FIN) AF: 0.353 AC: 3698 AN: 10470

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16546 AN: 67888

Other (OTH) AF: 0.324 AC: 682 AN: 2104

Alfa AF: 0.270 Hom.: 6388

Bravo AF: 0.343

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs195371; hg19: chr6-37304386;