rs10484515

chr6-163974368-C-A

Variant summary

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

The ENST00000659063.1(ENSG00000288696):n.43-34156C>A 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 0.261 in 151,924 control chromosomes in the GnomAD database, including 5,442 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 0.26 (5442 hom., cov: 32)
• Consequence: ENST00000659063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378102	XR_943213.4	n.558+54454C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659063.1	n.43-34156C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39607 AN: 151802 Hom.: 5432 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.261 AC: 39648 AN: 151924 Hom.: 5442 Cov.: 32 AF XY: 0.257 AC XY: 19061 AN XY: 74266

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.257

Alfa AF: 0.249 Hom.: 610

Bravo AF: 0.277

Asia WGS AF: 0.183 AC: 637 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484515; hg19: chr6-164395400;