6-82660735-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377876	XR_001744232.2	n.702+16404A>G		intron_variant	Intron 5 of 5
LOC105377876	XR_942739.2	n.566+16404A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;