chr6-35562369-A-C

Position:

• chr6-35562369-A-C

Variant summary

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

The XR_242006.4(LOC101929309):​n.181+17436A>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 0.045 in 152,292 control chromosomes in the GnomAD database, including 230 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 0.045 (230 hom., cov: 32)
• Consequence: LOC101929309 XR_242006.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

Genes affected

LOC101929309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929309	XR_242006.4	n.181+17436A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0449 AC: 6832 AN: 152174 Hom.: 230 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0310

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0249

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0450 AC: 6847 AN: 152292 Hom.: 230 Cov.: 32 AF XY: 0.0435 AC XY: 3239 AN XY: 74460

Gnomad4 AFR AF: 0.0978

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.0152

Gnomad4 NFE AF: 0.0249

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0292 Hom.: 92

Bravo AF: 0.0484

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
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: rs6917735; hg19: chr6-35530146;