chr21-38784351-G-C

Position:

• chr21-38784351-G-C

Variant summary

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

The XR_001755102.2(LOC107985480):​n.40+260G>C 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 0.6 in 152,120 control chromosomes in the GnomAD database, including 29,184 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 0.60 (29184 hom., cov: 33)
• Consequence: LOC107985480 XR_001755102.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

LOC107985480 (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 = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985480	XR_001755102.2	n.40+260G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91184 AN: 152002 Hom.: 29181 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.600 AC: 91219 AN: 152120 Hom.: 29184 Cov.: 33 AF XY: 0.602 AC XY: 44738 AN XY: 74356

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.597

Alfa AF: 0.647 Hom.: 4103

Bravo AF: 0.584

Asia WGS AF: 0.538 AC: 1874 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	0.14
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1209921; hg19: chr21-40156275;