6-82660735-T-C

Position:

• chr6-82660735-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001744232.2(LOC105377876):​n.702+16404A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725

Genes affected

LOC105377876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105377876	XR_001744232.2	n.702+16404A>G		intron_variant, non_coding_transcript_variant
LOC105377876	XR_942739.2	n.566+16404A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.879

Alfa AF: 0.883 Hom.: 55408

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs376096; hg19: chr6-83370452;