rs10484742

chr6-95961274-A-C

Variant summary

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

The ENST00000668456.1(ENSG00000287578):n.106-37124T>G 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 0.03 in 151,634 control chromosomes in the GnomAD database, including 207 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 0.030 (207 hom., cov: 32)
• Consequence: ENST00000668456.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986626	XR_001744263.2	n.148-37124T>G		intron_variant, non_coding_transcript_variant
LOC107986626	XR_001744264.2	n.148-37124T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668456.1	n.106-37124T>G		intron_variant, non_coding_transcript_variant
	ENST00000658251.1	n.76-37124T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4541 AN: 151516 Hom.: 204 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0113

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0279

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

GnomAD4 genome AF: 0.0300 AC: 4546 AN: 151634 Hom.: 207 Cov.: 32 AF XY: 0.0327 AC XY: 2423 AN XY: 74100

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0113

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0738

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0117

Gnomad4 OTH AF: 0.0276

Alfa AF: 0.0252 Hom.: 90

Bravo AF: 0.0389

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.0
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484742; hg19: chr6-96409150;