6-31568447-A-G

Position:

• chr6-31568447-A-G

Variant summary

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

The NR_149045.1(LOC100287329):​n.121+4136T>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 0.642 in 151,902 control chromosomes in the GnomAD database, including 31,677 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 0.64 (31677 hom., cov: 30)
• Consequence: LOC100287329 NR_149045.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287329	NR_149045.1	n.121+4136T>C		intron_variant, non_coding_transcript_variant
LTA	XM_047418773.1	c.-341-3045A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691266.1	n.118+4136T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97446 AN: 151784 Hom.: 31642 Cov.: 30

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.642 AC: 97534 AN: 151902 Hom.: 31677 Cov.: 30 AF XY: 0.643 AC XY: 47697 AN XY: 74224

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.641

Alfa AF: 0.599 Hom.: 33754

Bravo AF: 0.641

Asia WGS AF: 0.618 AC: 2150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	17
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844484; hg19: chr6-31536224;