chr6-82660735-T-C

Variant names:

• chr6-82660735-T-C
• rs376096
• XR_001744232.2:n.702+16404A>G

Variant summary

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

The XR_001744232.2(LOC105377876):​n.702+16404A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 149,552 control chromosomes in the GnomAD database, including 60,480 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 0.90 (60480 hom., cov: 24)
• Consequence: LOC105377876 XR_001744232.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725
• Publications: 2 publications found

Genes affected

LOC105377876 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.899 AC: 134383 AN: 149472 Hom.: 60441 Cov.: 24

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.891

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.899 AC: 134462 AN: 149552 Hom.: 60480 Cov.: 24 AF XY: 0.900 AC XY: 65627 AN XY: 72904

African (AFR) AF: 0.924 AC: 37457 AN: 40540

American (AMR) AF: 0.868 AC: 13038 AN: 15020

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3090 AN: 3462

East Asian (EAS) AF: 0.995 AC: 5036 AN: 5060

South Asian (SAS) AF: 0.913 AC: 4307 AN: 4716

European-Finnish (FIN) AF: 0.901 AC: 8957 AN: 9936

Middle Eastern (MID) AF: 0.889 AC: 256 AN: 288

European-Non Finnish (NFE) AF: 0.884 AC: 59734 AN: 67556

Other (OTH) AF: 0.879 AC: 1815 AN: 2066

Alfa AF: 0.885 Hom.: 73493

Bravo AF: 0.896

Asia WGS AF: 0.952 AC: 3308 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.46
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs376096; hg19: chr6-83370452;