rs9977677

Positions:

• chr21-36680485-G-A

Variant summary

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

The XR_007067857.1(LOC105369308):​n.83+18424C>T 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 0.346 in 151,916 control chromosomes in the GnomAD database, including 10,028 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 0.35 (10028 hom., cov: 31)
• Consequence: LOC105369308 XR_007067857.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

LOC105369308 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369308	XR_007067857.1	n.83+18424C>T		intron_variant, non_coding_transcript_variant
LOC105369308	XR_001755027.2	n.83+18424C>T		intron_variant, non_coding_transcript_variant
LOC105369308	XR_007067856.1	n.83+18424C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52539 AN: 151796 Hom.: 10026 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.346 AC: 52545 AN: 151916 Hom.: 10028 Cov.: 31 AF XY: 0.347 AC XY: 25797 AN XY: 74242

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.340

Alfa AF: 0.371 Hom.: 2144

Bravo AF: 0.329

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9977677; hg19: chr21-38052785;