rs7838490

Positions:

• chr8-88572819-G-A
• chr8-88572819-G-T

Variant summary

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

The ENST00000665922.1(ENSG00000253553):​n.324+30009G>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 0.198 in 151,936 control chromosomes in the GnomAD database, including 3,179 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 0.20 (3179 hom., cov: 32)
• Consequence: ENST00000665922.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375630	XR_001745653.3	n.355+30009G>A		intron_variant, non_coding_transcript_variant
LOC105375629	XR_928383.4	n.85-6707C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665922.1	n.324+30009G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30061 AN: 151818 Hom.: 3172 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.198 AC: 30087 AN: 151936 Hom.: 3179 Cov.: 32 AF XY: 0.197 AC XY: 14616 AN XY: 74232

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.203

Alfa AF: 0.182 Hom.: 4893

Bravo AF: 0.198

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7838490; hg19: chr8-89585048;