rs6912010

Variant names:

• chr6-110575441-G-A
• rs6912010
• XR_942866.3:n.24G>A

Variant summary

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

The XR_942866.3(LOC105377941):​n.24G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,106 control chromosomes in the GnomAD database, including 5,148 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 0.26 (5148 hom., cov: 33)
• Consequence: LOC105377941 XR_942866.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 2 publications found

Genes affected

LOC105377941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.255 AC: 38802 AN: 151988 Hom.: 5146 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.255 AC: 38819 AN: 152106 Hom.: 5148 Cov.: 33 AF XY: 0.254 AC XY: 18922 AN XY: 74352

African (AFR) AF: 0.276 AC: 11456 AN: 41504

American (AMR) AF: 0.218 AC: 3328 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3472

East Asian (EAS) AF: 0.157 AC: 811 AN: 5160

South Asian (SAS) AF: 0.218 AC: 1051 AN: 4820

European-Finnish (FIN) AF: 0.271 AC: 2864 AN: 10558

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17482 AN: 67992

Other (OTH) AF: 0.238 AC: 504 AN: 2114

Alfa AF: 0.255 Hom.: 3773

Bravo AF: 0.252

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.29
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6912010; hg19: chr6-110896644;