3-77901971-C-G

Position:

• chr3-77901971-C-G

Variant summary

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

The XR_940978.4(LOC105377171):​n.216-35883G>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 0.346 in 151,842 control chromosomes in the GnomAD database, including 10,107 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 (10107 hom., cov: 31)
• Consequence: LOC105377171 XR_940978.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

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 = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377171	XR_940978.4	n.216-35883G>C		intron_variant, non_coding_transcript_variant
LOC105377171	XR_940977.4	n.216-35883G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52441 AN: 151726 Hom.: 10094 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.346 AC: 52500 AN: 151842 Hom.: 10107 Cov.: 31 AF XY: 0.356 AC XY: 26443 AN XY: 74208

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.335

Alfa AF: 0.304 Hom.: 966

Bravo AF: 0.340

Asia WGS AF: 0.574 AC: 1996 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	0.69
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: rs11127608; hg19: chr3-77951122;