17-30245342-A-G

Variant names:

• chr17-30245342-A-G
• rs7214991
• ENST00000577420.2:n.259+6542A>G

Variant summary

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

The ENST00000577420.2(ENSG00000266120):​n.259+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 ENST00000577420.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 9 publications found

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577420.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266120	ENST00000577420.2	TSL:3	n.259+6542A>G		intron	N/A
	ENSG00000266120	ENST00000724730.1		n.258-4445A>G		intron	N/A
	ENSG00000266120	ENST00000724731.1		n.721-406A>G		intron	N/A

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

African (AFR) AF: 0.536 AC: 22208 AN: 41432

American (AMR) AF: 0.407 AC: 6216 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1147 AN: 5172

South Asian (SAS) AF: 0.364 AC: 1754 AN: 4820

European-Finnish (FIN) AF: 0.406 AC: 4284 AN: 10544

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25947 AN: 67950

Other (OTH) AF: 0.408 AC: 863 AN: 2116

Alfa AF: 0.390 Hom.: 16249

Bravo AF: 0.423

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.76
PhyloP100		-3.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7214991;

hg19: chr17-28572360;