3-16128121-A-C

Position:

• chr3-16128121-A-C

Variant summary

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

The ENST00000702609.1(ENSG00000287042):​n.197-9270A>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 0.061 in 152,086 control chromosomes in the GnomAD database, including 379 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 0.061 (379 hom., cov: 31)
• Consequence: ENST00000702609.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906217	XR_007095836.1	n.86-152T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702609.1	n.197-9270A>C		intron_variant, non_coding_transcript_variant
	ENST00000691919.2	n.240-9270A>C		intron_variant, non_coding_transcript_variant
	ENST00000702385.1	n.230-9270A>C		intron_variant, non_coding_transcript_variant
	ENST00000702645.1	n.549-9270A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0611 AC: 9279 AN: 151968 Hom.: 378 Cov.: 31

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0453

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0610 AC: 9283 AN: 152086 Hom.: 379 Cov.: 31 AF XY: 0.0623 AC XY: 4633 AN XY: 74328

Gnomad4 AFR AF: 0.0783

Gnomad4 AMR AF: 0.0400

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.0771

Gnomad4 FIN AF: 0.0627

Gnomad4 NFE AF: 0.0453

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0481 Hom.: 236

Bravo AF: 0.0608

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17041907; hg19: chr3-16169628;