chr4-89597881-A-G

Position:

• chr4-89597881-A-G

Variant summary

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

The ENST00000659878.1(ENSG00000251095):​n.479+9941A>G 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 0.163 in 152,184 control chromosomes in the GnomAD database, including 4,860 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 0.16 (4860 hom., cov: 32)
• Consequence: ENST00000659878.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377329	XR_007058469.1	n.301+9941A>G		intron_variant, non_coding_transcript_variant
LOC105377329	XR_007058467.1	n.301+9941A>G		intron_variant, non_coding_transcript_variant
LOC105377329	XR_007058468.1	n.301+9941A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659878.1	n.479+9941A>G		intron_variant, non_coding_transcript_variant
	ENST00000673949.1	n.306-11177T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24714 AN: 152066 Hom.: 4839 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0758

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0397

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0428

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.163 AC: 24772 AN: 152184 Hom.: 4860 Cov.: 32 AF XY: 0.159 AC XY: 11834 AN XY: 74418

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.0756

Gnomad4 ASJ AF: 0.0383

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0393

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0769 Hom.: 702

Bravo AF: 0.178

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.39
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7668883; hg19: chr4-90519032;