rs7221818

Positions:

• chr17-5898011-G-A
• chr17-5898011-G-C
• chr17-5898011-G-T

Variant summary

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

The NR_040000.1(LOC339166):​n.904+9181G>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 0.663 in 152,092 control chromosomes in the GnomAD database, including 33,883 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 0.66 (33883 hom., cov: 32)
• Consequence: LOC339166 NR_040000.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC339166	NR_040000.1	n.904+9181G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000563763.5	n.904+9181G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100762 AN: 151974 Hom.: 33845 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.663 AC: 100845 AN: 152092 Hom.: 33883 Cov.: 32 AF XY: 0.664 AC XY: 49341 AN XY: 74342

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.659

Alfa AF: 0.637 Hom.: 33545

Bravo AF: 0.658

Asia WGS AF: 0.728 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7221818; hg19: chr17-5801331;