rs6906804

Positions:

• chr6-1490347-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_427861.4(LOC102723944):​n.347+12104C>T 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 0.257 in 152,056 control chromosomes in the GnomAD database, including 5,596 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 (5596 hom., cov: 32)
• Consequence: LOC102723944 XR_427861.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932

Genes affected

LOC102723944 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723944	XR_427861.4	n.347+12104C>T		intron_variant, non_coding_transcript_variant
LOC105374883	XR_926387.3	n.265+404G>A		intron_variant, non_coding_transcript_variant
LOC105374883	XR_007059402.1	n.266-351G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38985 AN: 151938 Hom.: 5572 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.257 AC: 39061 AN: 152056 Hom.: 5596 Cov.: 32 AF XY: 0.263 AC XY: 19540 AN XY: 74316

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.282

Alfa AF: 0.214 Hom.: 6255

Bravo AF: 0.274

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	8.5
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6906804; hg19: chr6-1490582; COSMIC: COSV70073422;