6-35569629-T-C

Position:

• chr6-35569629-T-C

Variant summary

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

The XR_242006.4(LOC101929309):​n.182-23401T>C 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 0.823 in 152,146 control chromosomes in the GnomAD database, including 51,632 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 0.82 (51632 hom., cov: 33)
• Consequence: LOC101929309 XR_242006.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

LOC101929309 (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 (AMR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929309	XR_242006.4	n.182-23401T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125133 AN: 152028 Hom.: 51578 Cov.: 33

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.823 AC: 125242 AN: 152146 Hom.: 51632 Cov.: 33 AF XY: 0.823 AC XY: 61198 AN XY: 74396

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.794

Alfa AF: 0.813 Hom.: 19613

Bravo AF: 0.827

Asia WGS AF: 0.761 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.68
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3800374; hg19: chr6-35537406;