chr6-76702349-G-T

Position:

• chr6-76702349-G-T

Variant summary

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

The XR_942697.3(LOC105377861):​n.1125-2213C>A 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 0.188 in 151,626 control chromosomes in the GnomAD database, including 3,422 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 0.19 (3422 hom., cov: 31)
• Consequence: LOC105377861 XR_942697.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

LOC105377861 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377861	XR_942697.3	n.1125-2213C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28396 AN: 151508 Hom.: 3412 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0724

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.188 AC: 28430 AN: 151626 Hom.: 3422 Cov.: 31 AF XY: 0.186 AC XY: 13753 AN XY: 74082

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.183

Alfa AF: 0.134 Hom.: 2200

Bravo AF: 0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1457955; hg19: chr6-77412066;