rs7214991

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-30245342-A-C
• chr17-30245342-A-G
• chr17-30245342-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000577420.2(ENSG00000266120):​n.259+6542A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000266120 ENST00000577420.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 0 publications found

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000577420.2	n.259+6542A>C		intron_variant	Intron 1 of 2	3
ENSG00000266120	ENST00000724730.1	n.258-4445A>C		intron_variant	Intron 1 of 1
ENSG00000266120	ENST00000724731.1	n.721-406A>C		intron_variant	Intron 3 of 4
ENSG00000266120	ENST00000724732.1	n.171-1412A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.78
DANN	Benign	0.78
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs7214991; hg19: chr17-28572360;