chr3-77995538-G-A

Position:

• chr3-77995538-G-A

Variant summary

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

The XR_940978.4(LOC105377171):​n.215+27263C>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 0.338 in 151,524 control chromosomes in the GnomAD database, including 8,900 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 (8900 hom., cov: 31)
• Consequence: LOC105377171 XR_940978.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

Genes affected

LOC105377171 (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 (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377171	XR_940978.4	n.215+27263C>T		intron_variant, non_coding_transcript_variant
LOC105377171	XR_940977.4	n.215+27263C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51194 AN: 151406 Hom.: 8883 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.338 AC: 51244 AN: 151524 Hom.: 8900 Cov.: 31 AF XY: 0.334 AC XY: 24743 AN XY: 74034

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.319

Alfa AF: 0.348 Hom.: 14743

Bravo AF: 0.336

Asia WGS AF: 0.348 AC: 1209 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	0.37
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9836484; hg19: chr3-78044689;