rs6602217

chr10-6904301-T-C

Variant summary

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

The ENST00000664549.1(ENSG00000287277):n.568+30812A>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 0.148 in 152,084 control chromosomes in the GnomAD database, including 2,759 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 0.15 (2759 hom., cov: 32)
• Consequence: ENST00000664549.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376387	XR_007062046.1	n.851+16128A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664549.1	n.568+30812A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22421 AN: 151966 Hom.: 2754 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0767

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.148 AC: 22453 AN: 152084 Hom.: 2759 Cov.: 32 AF XY: 0.144 AC XY: 10741 AN XY: 74358

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.0912

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.0879

Gnomad4 NFE AF: 0.0768

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0840 Hom.: 1336

Bravo AF: 0.158

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.3
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6602217; hg19: chr10-6946263;