rs2215921

Positions:

• chr16-9603476-G-A
• chr16-9603476-G-C

Variant summary

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

The ENST00000634367.2(ENSG00000283003):​n.575-11045G>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 0.328 in 152,016 control chromosomes in the GnomAD database, including 9,086 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 0.33 (9086 hom., cov: 32)
• Consequence: ENST00000634367.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927026	XR_007064980.1	n.942+36886G>A		intron_variant, non_coding_transcript_variant
LOC101927026	XR_001752074.2	n.643+36886G>A		intron_variant, non_coding_transcript_variant
LOC101927026	XR_007064979.1	n.570+36886G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634367.2	n.575-11045G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49822 AN: 151898 Hom.: 9092 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.328 AC: 49824 AN: 152016 Hom.: 9086 Cov.: 32 AF XY: 0.326 AC XY: 24231 AN XY: 74298

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.351

Alfa AF: 0.381 Hom.: 22869

Bravo AF: 0.318

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215921; hg19: chr16-9697333;