17-30245342-A-G

Variant names:

• chr17-30245342-A-G
• rs7214991
• ENST00000577420.1:n.60+6542A>G

Variant summary

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

The ENST00000577420.1(ENSG00000266120):​n.60+6542A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,994 control chromosomes in the GnomAD database, including 14,063 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 0.42 (14063 hom., cov: 32)
• Consequence: ENSG00000266120 ENST00000577420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371720	XR_001752824.2	n.892-4445A>G		intron_variant	Intron 3 of 3
LOC105371720	XR_007065695.1	n.756-4445A>G		intron_variant	Intron 2 of 2
LOC105371720	XR_007065696.1	n.756-406A>G		intron_variant	Intron 2 of 2
LOC105371720	XR_007065698.1	n.755+6542A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000577420.1	n.60+6542A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63953 AN: 151876 Hom.: 14020 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.421 AC: 64054 AN: 151994 Hom.: 14063 Cov.: 32 AF XY: 0.418 AC XY: 31068 AN XY: 74280

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.408

Alfa AF: 0.384 Hom.: 12180

Bravo AF: 0.423

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7214991; hg19: chr17-28572360;