chr6-40928917-A-G

Position:

• chr6-40928917-A-G

Variant summary

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

The NR_110873.1(LOC101929555):​n.136-26219T>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 0.846 in 152,126 control chromosomes in the GnomAD database, including 54,674 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 0.85 (54674 hom., cov: 32)
• Consequence: LOC101929555 NR_110873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

Genes affected

LOC101929555 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929555	NR_110873.1	n.136-26219T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128644 AN: 152008 Hom.: 54661 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.846 AC: 128705 AN: 152126 Hom.: 54674 Cov.: 32 AF XY: 0.845 AC XY: 62873 AN XY: 74364

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.857

Alfa AF: 0.885 Hom.: 80449

Bravo AF: 0.843

Asia WGS AF: 0.811 AC: 2822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395760; hg19: chr6-40896656;