rs3105377

Variant names:

• chr7-69372016-C-T
• rs3105377
• ENST00000421513.1:n.273-12554G>A

Variant summary

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

The ENST00000421513.1(ENSG00000225718):​n.273-12554G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,002 control chromosomes in the GnomAD database, including 21,708 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 0.52 (21708 hom., cov: 33)
• Consequence: ENSG00000225718 ENST00000421513.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

ENSG00000225718 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225718	ENST00000421513.1	n.273-12554G>A		intron_variant	Intron 2 of 2	3
ENSG00000225718	ENST00000435148.1	n.156+58752G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79160 AN: 151884 Hom.: 21697 Cov.: 33

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.521 AC: 79190 AN: 152002 Hom.: 21708 Cov.: 33 AF XY: 0.515 AC XY: 38291 AN XY: 74296

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.509

Alfa AF: 0.570 Hom.: 4268

Bravo AF: 0.505

Asia WGS AF: 0.418 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3105377; hg19: chr7-68837002;