rs9918668

Positions:

• chr7-94062432-G-A
• chr7-94062432-G-C

Variant summary

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

The ENST00000415536.5(ENSG00000236453):​n.341+568G>A 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 0.465 in 152,056 control chromosomes in the GnomAD database, including 18,189 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 0.46 (18189 hom., cov: 32)
• Consequence: ENST00000415536.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986820	XR_001745270.3	n.4514+568G>A		intron_variant, non_coding_transcript_variant
LOC107986820	XR_001745271.3	n.4514+568G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000415536.5	n.341+568G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000438538.1	n.396+568G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70599 AN: 151940 Hom.: 18152 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.465 AC: 70686 AN: 152056 Hom.: 18189 Cov.: 32 AF XY: 0.463 AC XY: 34387 AN XY: 74326

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.422

Alfa AF: 0.393 Hom.: 12922

Bravo AF: 0.469

Asia WGS AF: 0.565 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9918668; hg19: chr7-93691744;