chr6-31560353-C-T

Position:

• chr6-31560353-C-T

Variant summary

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

The NR_149045.1(LOC100287329):​n.491G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,204 control chromosomes in the GnomAD database, including 1,004 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 0.11 (1004 hom., cov: 32)
• Consequence: LOC100287329 NR_149045.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100287329	NR_149045.1	n.491G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000691266.1	n.488G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16658 AN: 152086 Hom.: 1001 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.110 AC: 16686 AN: 152204 Hom.: 1004 Cov.: 32 AF XY: 0.113 AC XY: 8389 AN XY: 74414

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0955

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0363

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.118

Alfa AF: 0.102 Hom.: 1202

Bravo AF: 0.103

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
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: rs4947324; hg19: chr6-31528130;