rs17162294

chr7-9963989-C-T

Variant summary

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

The ENST00000663710.1(ENSG00000235431):n.200+2566C>T 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 0.099 in 152,128 control chromosomes in the GnomAD database, including 974 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 0.099 (974 hom., cov: 33)
• Consequence: ENST00000663710.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375146	XR_927023.3	n.355+2566C>T		intron_variant, non_coding_transcript_variant
LOC105375146	XR_927022.3	n.355+2566C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663710.1	n.200+2566C>T		intron_variant, non_coding_transcript_variant
	ENST00000451755.2	n.284+2566C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000671028.1	n.281+2566C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15029 AN: 152012 Hom.: 966 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.0977

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0990 AC: 15065 AN: 152128 Hom.: 974 Cov.: 33 AF XY: 0.102 AC XY: 7592 AN XY: 74376

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.0977

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0673 Hom.: 934

Bravo AF: 0.102

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	7.0
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17162294; hg19: chr7-10003616;