rs35678510

chr6-17066915-G-A

Variant summary

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

The XR_007059481.1(LOC124901269):n.39-6081C>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 0.0514 in 152,198 control chromosomes in the GnomAD database, including 279 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 0.051 (279 hom., cov: 33)
• Consequence: LOC124901269 XR_007059481.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

Genes affected

LOC124901269 (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 (NFE) allele frequency at 95% confidence interval = 0.0755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901269	XR_007059481.1	n.39-6081C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7822 AN: 152080 Hom.: 279 Cov.: 33

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.0794

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0514 AC: 7822 AN: 152198 Hom.: 279 Cov.: 33 AF XY: 0.0500 AC XY: 3719 AN XY: 74412

Gnomad4 AFR AF: 0.0140

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.0436

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00850

Gnomad4 FIN AF: 0.0794

Gnomad4 NFE AF: 0.0772

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0659 Hom.: 98

Bravo AF: 0.0469

Asia WGS AF: 0.00491 AC: 17 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.56
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35678510; hg19: chr6-17067146; COSMIC: COSV62123081;