rs7201988

chr16-9514649-C-G

Variant summary

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

The ENST00000652999.1(ENSG00000260071):n.284C>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,036 control chromosomes in the GnomAD database, including 8,994 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 0.34 (8992 hom., cov: 31)
  • Exomes 𝑓: 0.19 (2 hom.)
• Consequence: ENST00000652999.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927026	XR_007064980.1	n.418-50C>G		intron_variant, non_coding_transcript_variant
LOC101927026	XR_002957870.1	n.1006-50C>G		intron_variant, non_coding_transcript_variant
LOC101927026	XR_933053.3	n.426-50C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652999.1	n.284C>G		splice_region_variant, non_coding_transcript_exon_variant	4/5

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51247 AN: 151846 Hom.: 8988 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.194 AC: 14 AN: 72 Hom.: 2 Cov.: 0 AF XY: 0.203 AC XY: 13 AN XY: 64

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.337 AC: 51266 AN: 151964 Hom.: 8992 Cov.: 31 AF XY: 0.339 AC XY: 25197 AN XY: 74282

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.338

Alfa AF: 0.309 Hom.: 926

Bravo AF: 0.349

Asia WGS AF: 0.371 AC: 1293 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	0.56
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7201988; hg19: chr16-9608506;