rs10484810

Positions:

• chr6-139963540-C-A
• chr6-139963540-C-T

Variant summary

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

The ENST00000666152.1(ENSG00000287820):​n.747+14472G>T 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 0.108 in 152,160 control chromosomes in the GnomAD database, including 1,992 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 (1992 hom., cov: 32)
• Consequence: ENST00000666152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666152.1	n.747+14472G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16348 AN: 152042 Hom.: 1997 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.108 AC: 16361 AN: 152160 Hom.: 1992 Cov.: 32 AF XY: 0.106 AC XY: 7903 AN XY: 74410

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0409

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0268

Gnomad4 OTH AF: 0.0994

Alfa AF: 0.0360 Hom.: 139

Bravo AF: 0.117

Asia WGS AF: 0.0330 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484810; hg19: chr6-140284677;