9-7925381-T-G

Position:

• chr9-7925381-T-G

Variant summary

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

The ENST00000668681.1(ENSG00000231902):​n.566+164A>C 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 0.416 in 151,966 control chromosomes in the GnomAD database, including 13,708 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 (13708 hom., cov: 32)
• Consequence: ENST00000668681.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375971	XR_929463.3	n.670+164A>C		intron_variant, non_coding_transcript_variant
LOC105375971	XR_929462.3	n.670+164A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668681.1	n.566+164A>C		intron_variant, non_coding_transcript_variant
	ENST00000656028.1	n.702+164A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63184 AN: 151848 Hom.: 13702 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.416 AC: 63229 AN: 151966 Hom.: 13708 Cov.: 32 AF XY: 0.419 AC XY: 31110 AN XY: 74252

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.412

Alfa AF: 0.408 Hom.: 27517

Bravo AF: 0.429

Asia WGS AF: 0.542 AC: 1881 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	14
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535480; hg19: chr9-7925381;