rs6602217

Variant names:

• chr10-6904301-T-C
• rs6602217
• ENST00000457632.1:n.45-12344A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000457632.1(ENSG00000287277):​n.45-12344A>G variant causes a intron 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: ENSG00000287277 ENST00000457632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 7 publications found

Genes affected

ENSG00000287277 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105376387	NR_188183.1	n.568+30812A>G		intron_variant	Intron 3 of 4
LOC105376387	NR_188184.1	n.370+30812A>G		intron_variant	Intron 2 of 4
LOC105376387	NR_188185.1	n.370+30812A>G		intron_variant	Intron 2 of 4
LOC105376387	NR_188186.1	n.370+30812A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287277	ENST00000457632.1	n.45-12344A>G		intron_variant	Intron 1 of 2	3
ENSG00000287277	ENST00000652889.2	n.419+30812A>G		intron_variant	Intron 2 of 3
ENSG00000287277	ENST00000654694.1	n.376+30812A>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.339 AC: 14034 AN: 41444

American (AMR) AF: 0.0912 AC: 1394 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4816

European-Finnish (FIN) AF: 0.0879 AC: 930 AN: 10576

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0768 AC: 5219 AN: 67998

Other (OTH) AF: 0.132 AC: 279 AN: 2106

Alfa AF: 0.0978 Hom.: 3361

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
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs6602217; hg19: chr10-6946263;