6-84779898-C-T

Position:

• chr6-84779898-C-T

Variant summary

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

The XR_007059927.1(LOC124901494):​n.247+5846C>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 0.398 in 151,980 control chromosomes in the GnomAD database, including 14,097 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 0.40 (14097 hom., cov: 31)
• Consequence: LOC124901494 XR_007059927.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

Genes affected

LOC124901494 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901494	XR_007059927.1	n.247+5846C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60423 AN: 151860 Hom.: 14095 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.398 AC: 60446 AN: 151980 Hom.: 14097 Cov.: 31 AF XY: 0.403 AC XY: 29947 AN XY: 74272

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.416

Alfa AF: 0.456 Hom.: 4124

Bravo AF: 0.375

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs215935; hg19: chr6-85489616;